WorldWideScience

Sample records for crystal microbalance dna

  1. Data Acquisition System for Quartz Crystal Microbalances

    Directory of Open Access Journals (Sweden)

    Kleber Romero Felizardo

    2006-02-01

    Full Text Available This work presents a data acquisition system used in a mass sensor: quartz crystal microbalance. This system reads the frequency of this sensor along the time and sends the collected data to the computer through a serial interface.

  2. Construction of simple quartz crystal microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Ristov, Milcho [Center of Energy, Informatics and Materials of the Macedonian Academy fo Science and Arts, Skopje (Macedonia, The Former Yugoslav Republic of); Mitrevski, Mitre [Institute of Physics, Faculty of natural Science and Mathematics, Ss Cyril and Methodius University, Skopje (Macedonia, The Former Yugoslav Republic of)

    2003-07-01

    A very simple Quartz Crystal Microbalance (QCM) was constructed for the measurement of thickness of chemically deposited thin films. QCM consisted of two active elements: one dual-gate MOSFET and one bipolar transistor, and as usually two AT-cut quartz crystal. The beat frequency oscillation generated as a result of loading of the sensor crystal by the deposited thin film, was measured by HP-multimeter, set as a low frequency meter. The sensitivity was found to be high and satisfactory for the study of growth rate of thin films, mainly deposited by methods of chemical deposition.

  3. Construction of simple quartz crystal microbalance

    International Nuclear Information System (INIS)

    Ristov, Milcho; Mitrevski, Mitre

    2002-01-01

    A very simple Quartz Crystal Microbalance (QCM) was constructed for the measurement of thickness of chemically deposited thin films. QCM consisted of two active elements: one dual-gate MOSFET and one bipolar transistor, and as usually two AT-cut quartz crystal. The beat frequency oscillation generated as a result of loading of the sensor crystal by the deposited thin film, was measured by HP-multimeter, set as a low frequency meter. The sensitivity was found to be high and satisfactory for the study of growth rate of thin films, mainly deposited by methods of chemical deposition.

  4. A method of layer-by-layer gold nanoparticle hybridization in a quartz crystal microbalance DNA sensing system used to detect dengue virus

    International Nuclear Information System (INIS)

    Chen, S-H; Chuang, Y-C; Lu, Y-C; Lin, H-C; Yang, Y-L; Lin, C-S

    2009-01-01

    Dengue virus (DENV) is nowadays the most important arthropod-spread virus affecting humans existing in more than 100 countries worldwide. A rapid and sensitive detection method for the early diagnosis of infectious dengue virus urgently needs to be developed. In the present study, a circulating-flow quartz crystal microbalance (QCM) biosensing method combining oligonucleotide-functionalized gold nanoparticles (i.e. AuNP probes) used to detect DENV has been established. In the DNA-QCM method, two kinds of specific AuNP probes were linked by the target sequences onto the QCM chip to amplify the detection signal, i.e. oscillatory frequency change (ΔF) of the QCM sensor. The target sequences amplified from the DENV genome act as a bridge for the layer-by-layer AuNP probes' hybridization in the method. Besides being amplifiers of the detection signal, the specific AuNP probes used in the DNA-QCM method also play the role of verifiers to specifically recognize their target sequences in the detection. The effect of four AuNP sizes on the layer-by-layer hybridization has been evaluated and it is found that 13 nm AuNPs collocated with 13 nm AuNPs showed the best hybridization efficiency. According to the nanoparticle application, the DNA-QCM biosensing method was able to detect dengue viral RNA in virus-contaminated serum as plaque titers being 2 PFU ml -1 and a linear correlation (R 2 = 0.987) of ΔF versus virus titration from 2 x 10 0 to 2 x 10 6 PFU ml -1 was found. The sensitivity and specificity of the present DNA-QCM method with nanoparticle technology showed it to be comparable to the fluorescent real-time PCR methods. Moreover, the method described herein was shown to not require expensive equipment, was label-free and highly sensitive.

  5. A method of layer-by-layer gold nanoparticle hybridization in a quartz crystal microbalance DNA sensing system used to detect dengue virus

    Energy Technology Data Exchange (ETDEWEB)

    Chen, S-H; Chuang, Y-C; Lu, Y-C; Lin, H-C; Yang, Y-L; Lin, C-S [Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan (China)], E-mail: lincs@mail.nctu.edu.tw

    2009-05-27

    Dengue virus (DENV) is nowadays the most important arthropod-spread virus affecting humans existing in more than 100 countries worldwide. A rapid and sensitive detection method for the early diagnosis of infectious dengue virus urgently needs to be developed. In the present study, a circulating-flow quartz crystal microbalance (QCM) biosensing method combining oligonucleotide-functionalized gold nanoparticles (i.e. AuNP probes) used to detect DENV has been established. In the DNA-QCM method, two kinds of specific AuNP probes were linked by the target sequences onto the QCM chip to amplify the detection signal, i.e. oscillatory frequency change ({delta}F) of the QCM sensor. The target sequences amplified from the DENV genome act as a bridge for the layer-by-layer AuNP probes' hybridization in the method. Besides being amplifiers of the detection signal, the specific AuNP probes used in the DNA-QCM method also play the role of verifiers to specifically recognize their target sequences in the detection. The effect of four AuNP sizes on the layer-by-layer hybridization has been evaluated and it is found that 13 nm AuNPs collocated with 13 nm AuNPs showed the best hybridization efficiency. According to the nanoparticle application, the DNA-QCM biosensing method was able to detect dengue viral RNA in virus-contaminated serum as plaque titers being 2 PFU ml{sup -1} and a linear correlation (R{sup 2} = 0.987) of {delta}F versus virus titration from 2 x 10{sup 0} to 2 x 10{sup 6} PFU ml{sup -1} was found. The sensitivity and specificity of the present DNA-QCM method with nanoparticle technology showed it to be comparable to the fluorescent real-time PCR methods. Moreover, the method described herein was shown to not require expensive equipment, was label-free and highly sensitive.

  6. Recent Advances in Quartz Crystal Microbalance-Based Sensors

    Directory of Open Access Journals (Sweden)

    Sandeep Kumar Vashist

    2011-01-01

    Full Text Available Quartz crystal microbalance (QCM has gained exceptional importance in the fields of (biosensors, material science, environmental monitoring, and electrochemistry based on the phenomenal development in QCM-based sensing during the last two decades. This review provides an overview of recent advances made in QCM-based sensors, which have been widely employed in a plethora of applications for the detection of chemicals, biomolecules and microorganisms.

  7. Electronic Nose using Gas Chromatography Column and Quartz Crystal Microbalance

    Directory of Open Access Journals (Sweden)

    Hari Agus Sujono

    2011-08-01

    Full Text Available The conventional electronic nose usually consists of an array of dissimilar chemical sensors such as quartz crystal microbalance (QCM combined with pattern recognition algorithm such as Neural network. Because of parallel processing, the system needs a huge number of sensors and circuits which may emerge complexity and inter-channel crosstalk problems. In this research, a new type of odor identification which combines between gas chromatography (GC and electronic nose methods has been developed. The system consists of a GC column and a 10-MHz quartz crystal microbalance sensor producing a unique pattern for an odor in time domain. This method offers advantages of substantially reduced size, interferences and power consumption in comparison to existing odor identification system. Several odors of organic compounds were introduced to evaluate the selectivity of the system. Principle component analysis method was used to visualize the classification of each odor in two-dimensional space. This system could resolve common organic solvents, including molecules of different classes (aromatic from alcohols as well as those within a particular class (methanol from ethanol and also fuels (premium from pertamax. The neural network can be taught to recognize the odors tested in the experiment with identification rate of 85 %. It is therefore the system may take the place of human nose, especially for poisonous odor evaluations.

  8. A quartz crystal microbalance dew point sensor without frequency measurement

    Science.gov (United States)

    Wang, Guohua; Zhang, Weishuo; Wang, Shuo; Sun, Jinglin

    2014-11-01

    This work deals with the design of a dew point sensor based on Quartz Crystal Microbalance (QCM) without measuring the frequency. This idea is inspired by the fact that the Colpitts oscillation circuit will stop oscillating when the QCM works in the liquid media. The quartz crystal and the electrode are designed through the finite element simulation and the stop oscillating experiment is conducted to verify the sensibility. Moreover, the measurement result is calibrated to approach the true value. At last a series of dew points at the same temperature is measured with the designed sensor. Results show that the designed dew point sensor is able to detect the dew point with the proper accuracy.

  9. Using Quartz Crystal Microbalance for Field Measurement of Liquid Viscosities

    Directory of Open Access Journals (Sweden)

    Qingsong Bai

    2016-01-01

    Full Text Available The field measurement of liquid viscosities, especially the high viscous liquids, is challenging and often requires expensive equipment, long processing time, and lots of reagent. We use quartz crystal microbalances (QCMs operating in solution which are also sensitive to the viscosity and density of the contacting solution. QCMs are typically investigated for sensor applications in which one surface of QCM completely immersed in Newtonian liquid, but the viscous damping in liquids would cause not only large frequency shifts but also large losses in the quality factor Q leading to instability and even cessation of oscillation. A novel mass-sensitivity-based method for field measurement of liquid viscosities using a QCM is demonstrated in this paper and a model describing the influence of the liquid properties on the oscillation frequency is established as well. Two groups of verified experiments were performed and the experimental results show that the presented method is effective and possesses potential applications.

  10. Respiratory Monitoring by Porphyrin Modified Quartz Crystal Microbalance Sensors

    Directory of Open Access Journals (Sweden)

    Seung-Woo Lee

    2011-01-01

    Full Text Available A respiratory monitoring system based on a quartz crystal microbalance (QCM sensor with a functional film was designed and investigated. Porphyrins 5,10,15,20-tetrakis-(4-sulfophenyl-21H,23H-porphine (TSPP and 5,10,15,20-tetrakis-(4-sulfophenyl-21H, 23H-porphine manganese (III chloride (MnTSPP used as sensitive elements were assembled with a poly(diallyldimethyl ammonium chloride (PDDA. Films were deposited on the QCM resonators using layer-by-layer method in order to develop the sensor. The developed system, in which the sensor response reflects lung movements, was able to track human respiration providing respiratory rate (RR and respiratory pattern (RP. The sensor system was tested on healthy volunteers to compare RPs and calculate RRs. The operation principle of the proposed system is based on the fast adsorption/desorption behavior of water originated from human breath into the sensor films deposited on the QCM electrode.

  11. Data analysis for lidar and quartz crystal microbalance systems

    Science.gov (United States)

    Kent, G. S.; Deepak, A.

    1985-01-01

    Results are presented of the analysis of data taken on the stratospheric aerosol, using lidar, Quartz Crystal Microbalance (QCM), and the SAGE and SAM II satellite systems. The main objective of the work reported has been to use the data, taken with the NASA-LaRC instruments to study the stratospheric effects of volcanic eruptions during the period between the launch of the SAGE and SAM II satellite systems and October 1980. Four significant volcanic eruptions, for which data are available, occurred during this period--Soufriere, Sierra Negra, Mt. St. Helens, and Ulawun. Data on these have been analyzed to determine the changes in stratospheric mass loading produced by the eruptions, and to study the dispersion of the newly injected material.

  12. Electroacoustic polymer microchip as an alternative to quartz crystal microbalance for biosensor development.

    Science.gov (United States)

    Gamby, Jean; Lazerges, Mathieu; Girault, Hubert H; Deslouis, Claude; Gabrielli, Claude; Perrot, Hubert; Tribollet, Bernard

    2008-12-01

    Laser photoablation of poly(ethylene terephthalate) (PET), a flexible dielectric organic polymer, was used to design an acoustic miniaturized DNA biosensor. The microchip device includes a 100-microm-thick PET layer, with two microband electrodes patterned in photoablated microchannels on one side and a depressed photoablated disk decorated by gold sputtered layer on the other side. Upon application of an electric signal between the two electrodes, an electroacoustic resonance phenomenon at approximately 30 MHz was established through the microelectrodes/PET/ gold layer interface. The electroacoustic resonance response was fitted with a series RLC motional arm in parallel with a static Co arm of a Buttlerworth-Van Dyke equivalent circuit: admittance spectra recorded after successive cycles of DNA hybridization on the gold surface showed reproducible changes on R, L, and C parameters. The same hybridizations runs were performed concomitantly on a 27-MHz (9 MHz, third overtone) quartz crystal microbalance in order to validate the PET device developed for bioanalysis applications. The electroacoustic PET device, approximately 100 times smaller than a microbalance quartz crystal, is interesting for the large-scale integration of acoustic sensors in biochips.

  13. Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM Sensors

    Directory of Open Access Journals (Sweden)

    Sibel Emir Diltemiz

    2017-02-01

    Full Text Available Molecularly imprinted polymers (MIPs as artificial antibodies have received considerable scientific attention in the past years in the field of (biosensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.. On the other hand, the Quartz Crystal Microbalance (QCM is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (biosensor systems based on QCMs combined with molecular imprinting technology.

  14. Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors

    Science.gov (United States)

    Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

    2017-01-01

    Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology. PMID:28245588

  15. Quartz crystal microbalance sensor using ionophore for ammonium ion detection.

    Science.gov (United States)

    Kosaki, Yasuhiro; Takano, Kosuke; Citterio, Daniel; Suzuki, Koji; Shiratori, Seimei

    2012-01-01

    Ionophore-based quartz crystal microbalance (QCM) ammonium ion sensors with a detection limit for ammonium ion concentrations as low as 2.2 microM were fabricated. Ionophores are molecules, which selectively bind a particular ion. In this study, one of the known ionophores for ammonium, nonactin, was used to detect ammonium ions for environmental in-situ monitoring of aquarium water for the first time. To fabricate the sensing films, poly(vinyl chloride) was used as the matrix for the immobilization of nonactin. Furthermore, the anionic additive, tetrakis (4-chlorophenyl) borate potassium salt and the plasticizer dioctyl sebacate were used to enhance the sensor properties. The sensor allowed detecting ammonium ions not only in static solution, but also in flowing water. The sensor showed a nearly linear response with the increase of the ammonium ion concentration. The QCM resonance frequency increased with the increase of ammonium ion concentration, suggesting a decreasing weight of the sensing film. The detailed response mechanism could not be verified yet. However, from the results obtained when using a different plasticizer, nitrophenyl octyl ether, it is considered that this effect is caused by the release of water molecules. Consequently, the newly fabricated sensor detects ammonium ions by discharge of water. It shows high selectivity over potassium and sodium ions. We conclude that the newly fabricated sensor can be applied for detecting ammonium ions in aquarium water, since it allows measuring low ammonium ion concentrations. This sensor will be usable for water quality monitoring and controlling.

  16. Quartz crystal microbalance (QCM) affinity biosensor for genetically modified organisms (GMOs) detection.

    Science.gov (United States)

    Mannelli, Ilaria; Minunni, Maria; Tombelli, Sara; Mascini, Marco

    2003-03-01

    A DNA piezoelectric sensor has been developed for the detection of genetically modified organisms (GMOs). Single stranded DNA (ssDNA) probes were immobilised on the sensor surface of a quartz crystal microbalance (QCM) device and the hybridisation between the immobilised probe and the target complementary sequence in solution was monitored. The probe sequences were internal to the sequence of the 35S promoter (P) and Nos terminator (T), which are inserted sequences in the genome of GMOs regulating the transgene expression. Two different probe immobilisation procedures were applied: (a) a thiol-dextran procedure and (b) a thiol-derivatised probe and blocking thiol procedure. The system has been optimised using synthetic oligonucleotides, which were then applied to samples of plasmidic and genomic DNA isolated from the pBI121 plasmid, certified reference materials (CRM), and real samples amplified by the polymerase chain reaction (PCR). The analytical parameters of the sensor have been investigated (sensitivity, reproducibility, lifetime etc.). The results obtained showed that both immobilisation procedures enabled sensitive and specific detection of GMOs, providing a useful tool for screening analysis in food samples.

  17. The quartz crystal microbalance in soft matter research fundamentals and modeling

    CERN Document Server

    Johannsmann, Diethelm

    2014-01-01

    This book describes the physics of the second-generation quartz crystal microbalance (QCM), a fundamental method of analysis for soft matter at interfaces.From a device for measuring film thickness in vacuum, the quartz crystal microbalance (QCM) has in the past two decades evolved into a versatile instrument for analyzing soft matter at solid/liquid and solid/gas interfaces that found applications in diverse fields including the life sciences, material science, polymer research and electrochemistry. As a consequence of this success, the QCM is now being used by scientists with a wide variety

  18. Functional Durability of a Quartz Crystal Microbalance Sensor for the Rapid Detection of Salmonella in Liquids from Poultry Packaging

    National Research Council Canada - National Science Library

    Olsen, Eric

    2000-01-01

    .... A rapid, sensitive (350 +/- 150 cells ml/cm) quartz crystal microbalance biosensor, layered with heat-treated anti-Salmonella-phospholipid monolayers by the Langmuir-Blodgett technique, has been evaluated by immersion testing in chicken exudate...

  19. Quartz Crystal Microbalance: A tool for analyzing loss of volatile compounds, gas sorption, and curing kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Bajric, Sendin [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-03-16

    Los Alamos National Laboratory (LANL) has recently procured a quartz crystal microbalance (QCM). Current popular uses are biological sensors, surface chemistry, and vapor detection. LANL has projects related to analyzing curing kinetics, measuring gas sorption on polymers, and analyzing the loss of volatile compounds in polymer materials. The QCM has yet to be employed; however, this review will cover the use of the QCM in these applications and its potential.

  20. Quartz Crystal Microbalance Studies Of Dimethyl Methylphosphonate Sorption Into Trisilanolphenyl-Poss Films

    Science.gov (United States)

    2006-11-06

    QUARTZ CRYSTAL MICROBALANCE STUDIES OF DIMETHYL METHYLPHOSPHONATE SORPTION INTO TRISILANOLPHENYL-POSS FILMS Joshua D. Kittle Thesis ...subsequent DIMP layers form a solid- like phase as a result of nucleated growth around the first layer. Bertilsson et al. studied the adsorption of...of QCMs in liquids,55, 56 opening the door to a variety of applications, including the study of electrodeposition of metals,57,65 electrochemical

  1. Studies of jet fuel additives using the quartz crystal microbalance and pressure monitoring at 140 C

    Energy Technology Data Exchange (ETDEWEB)

    Zabarnick, S.; Grinstead, R.R. [Univ. of Dayton Research Institute, OH (United States)

    1995-05-01

    The quartz crystal microbalance (QCM) and pressure monitoring are used for the evaluation of jet fuel additives for the improvement of jet fuel thermal stability. The mechanisms of additive behavior are determined by measuring the time dependent deposition with the QCM and oxidation by pressure measurements. Studies at various additive concentrations permits the determination of optimum additive concentrations. Additive packages made of mixtures of antioxidants, detergent/dispersants, and metal deactivators are shown to yield good improvements in thermal stability over a wide range of jet fuel types.

  2. Epoxy Resin Modified Quartz Crystal Microbalance Sensor for Chemical Warfare Agent Sulfur Mustard Vapor Detection

    Directory of Open Access Journals (Sweden)

    Rajendra BUNKAR

    2010-02-01

    Full Text Available An epoxy resin polymer coated quartz crystal microbalance (PC-QCM is used for detection of sulfur mustard vapor (SM. When SM vapor is exposed to PC-QCM sensor frequency shift is observed. The response of the sensor in ambient condition is 554 Hz with ±10 % variation upon exposure of 155 ppm of the SM concentration. The observed response loss is nearly 40 % over the period of 15 months. The response of the sensor is higher for SM than compare to structurally similar chloroethyl ether (CEE and other interferences.

  3. Investigating calcite growth rates using a quartz crystal microbalance with dissipation (QCM-D)

    Science.gov (United States)

    Cao, Bo; Stack, Andrew G.; Steefel, Carl I.; DePaolo, Donald J.; Lammers, Laura N.; Hu, Yandi

    2018-02-01

    Calcite precipitation plays a significant role in processes such as geological carbon sequestration and toxic metal sequestration and, yet, the rates and mechanisms of calcite growth under close to equilibrium conditions are far from well understood. In this study, a quartz crystal microbalance with dissipation (QCM-D) was used for the first time to measure macroscopic calcite growth rates. Calcite seed crystals were first nucleated and grown on sensors, then growth rates of calcite seed crystals were measured in real-time under close to equilibrium conditions (saturation index, SI = log ({Ca2+}/{CO32-}/Ksp) = 0.01-0.7, where {i} represent ion activities and Ksp = 10-8.48 is the calcite thermodynamic solubility constant). At the end of the experiments, total masses of calcite crystals on sensors measured by QCM-D and inductively coupled plasma mass spectrometry (ICP-MS) were consistent, validating the QCM-D measurements. Calcite growth rates measured by QCM-D were compared with reported macroscopic growth rates measured with auto-titration, ICP-MS, and microbalance. Calcite growth rates measured by QCM-D were also compared with microscopic growth rates measured by atomic force microscopy (AFM) and with rates predicted by two process-based crystal growth models. The discrepancies in growth rates among AFM measurements and model predictions appear to mainly arise from differences in step densities, and the step velocities were consistent among the AFM measurements as well as with both model predictions. Using the predicted steady-state step velocity and the measured step densities, both models predict well the growth rates measured using QCM-D and AFM. This study provides valuable insights into the effects of reactive site densities on calcite growth rate, which may help design future growth models to predict transient-state step densities.

  4. Measurement of Total Condensation on a Shrouded Cryogenic Surface using a Single Quart Crystal Microbalance

    International Nuclear Information System (INIS)

    Haid, B.J.; Malsbury, T.N.; Gibson, C.R.; Warren, C.T.

    2008-01-01

    A single quartz crystal microbalance (QCM) is cooled to 18 K to measure condensation rates inside of a retractable ''shroud'' enclosure. The shroud is of a design intended to minimize condensate on fusion targets to be fielded at the National Ignition Facility (NIF). The shroud has a double-wall construction with an inner wall that may be cooled to 75-100 K. The QCM and the shroud system were mounted in a vacuum chamber and cooled using a cryocooler. Condensation rates were measured at various vacuum levels and compositions, and with the shroud open or closed. A technique for measuring total condensate during the cooldown of the system with an accuracy of better than 1.0 x 10 -6 g/cm 2 was also demonstrated. The technique involved a separate measurement of the condensate-free crystal frequency as a function of temperature that was later applied to the measurement of interest

  5. Note: A dual-channel sensor for dew point measurement based on quartz crystal microbalance

    Science.gov (United States)

    Li, Ning; Meng, Xiaofeng; Nie, Jing

    2017-05-01

    A new sensor with dual-channel was designed for eliminating the temperature effect on the frequency measurement of the quartz crystal microbalance (QCM) in dew point detection. The sensor uses active temperature control, produces condensation on the surface of QCM, and then detects the dew point. Both the single-channel and the dual-channel methods were conducted based on the device. The measurement error of the single-channel method was less than 0.5 °C at the dew point range of -2 °C-10 °C while the dual-channel was 0.3 °C. The results showed that the dual-channel method was able to eliminate the temperature effect and yield better measurement accuracy.

  6. Polyacrylonitrile Nanofiber-Based Quartz Crystal Microbalance for Sensitive Detection of Safrole

    Directory of Open Access Journals (Sweden)

    Aditya Rianjanu

    2018-04-01

    Full Text Available Safrole is the main precursor for producing the amphetamine-type stimulant (ATS drug, N-methyl-3,4-methylenedioxyamphetamine (MDMA, also known as ecstasy. We devise a polyacrylonitrile (PAN nanofiber-based quartz crystal microbalance (QCM for detecting safrole. The PAN nanofibers were fabricated by direct electrospinning to modify the QCM chips. The PAN nanofiber on the QCM chips has a diameter of 240 ± 10 nm. The sensing of safrole by QCM modified with PAN nanofiber shows good reversibility and an apparent sensitivity of 4.6 Hz·L/mg. The proposed method is simple, inexpensive, and convenient for detecting safrole, and can be an alternative to conventional instrumental analytical methods for general volatile compounds.

  7. Separate density and viscosity measurements of unknown liquid using quartz crystal microbalance

    Directory of Open Access Journals (Sweden)

    Feng Tan

    2016-09-01

    Full Text Available Aqueous liquids have a wide range of applications in many fields. Basic physical properties like the density and the viscosity have great impacts on the functionalities of a given ionic liquid. For the millions kinds of existing liquids, only a few have been systematically measured with the density and the viscosity using traditional methods. However, these methods are limited to measure the density and the viscosity of an ionic liquid simultaneously especially in processing micro sample volumes. To meet this challenge, we present a new theoretical model and a novel method to separate density and viscosity measurements with single quartz crystal microbalance (QCM in this work. The agreement of experimental results and theocratical calculations shows that the QCM is capable to measure the density and the viscosity of ionic liquids.

  8. Quartz crystal microbalance-based system for high-sensitivity differential sputter yield measurements

    International Nuclear Information System (INIS)

    Rubin, B.; Topper, J. L.; Farnell, C. C.; Yalin, A. P.

    2009-01-01

    We present a quartz crystal microbalance-based system for high sensitivity differential sputter yield measurements of different target materials due to ion bombardment. The differential sputter yields can be integrated to find total yields. Possible ion beam conditions include ion energies in the range of 30-350 eV and incidence angles of 0 deg. - 70 deg. from normal. A four-grid ion optics system is used to achieve a collimated ion beam at low energy (<100 eV) and a two-grid ion optics is used for higher energies (up to 750 eV). A complementary weight loss approach is also used to measure total sputter yields. Validation experiments are presented that confirm high sensitivity and accuracy of sputter yield measurements.

  9. Alcohol vapours sensor based on thin polyaniline salt film and quartz crystal microbalance.

    Science.gov (United States)

    Ayad, Mohamad M; Torad, Nagy L

    2009-06-15

    A sensor based on the quartz crystal microbalance (QCM) technique was developed for detection of a number of primary aliphatic alcohols such as ethanol, methanol, 1-propanol, and 2-propanol vapours. Detection was based on a sensitive and a thin film of polyaniline, emeraldine salt (ES), coated the QCM electrode. The frequency shifts (Delta f) of the QCM were increased due to the vapour absorption into the ES film. The values of Delta f were found to be linearly correlated with the concentrations of alcohols vapour in mg L(-1). The changes in frequency are due to the hydrophilic character of the ES and the electrostatic interaction as well as the type of the alcohol. The sensor shows a good reproducibility and reversibility. The diffusion and diffusion coefficient (D) of different alcohols vapour were determined. It was found that the sensor follows Fickian kinetics.

  10. A sensor of alcohol vapours based on thin polyaniline base film and quartz crystal microbalance.

    Science.gov (United States)

    Ayad, Mohamad M; El-Hefnawey, Gad; Torad, Nagy L

    2009-08-30

    Thin films of polyaniline base, emeraldine base (EB), coating on the quartz crystal microbalance (QCM) electrode were used as a sensitive layer for the detection of a number of primary aliphatic alcohols such as ethanol, methanol, 2-propanol and 1-propanol vapours. The frequency shifts (Deltaf) of the QCM were increased due to the vapour adsorption into the EB film. Deltaf were found to be linearly correlated with the concentrations of alcohols vapour in part per million (ppm). The sensitivity of the sensor was found to be governed by the chemical structure of the alcohol. The sensor shows a good reproducibility and reversibility. The diffusions of different alcohols vapour were studied and the diffusion coefficients (D) were calculated. It is concluded that the diffusion of the vapours into the EB film follows Fickian kinetics.

  11. Towards vibrational spectroscopy on surface-attached colloids performed with a quartz crystal microbalance

    Directory of Open Access Journals (Sweden)

    Diethelm Johannsmann

    2016-12-01

    Full Text Available Colloidal spheres attached to a quartz crystal microbalance (QCM produce the so-called “coupled resonances”. They are resonators of their own, characterized by a particle resonance frequency, a resonance bandwidth, and a modal mass. When the frequency of the main resonator comes close to the frequency of the coupled resonance, the bandwidth goes through a maximum. A coupled resonance can be viewed as an absorption line in acoustic shear-wave spectroscopy. The known concepts from spectroscopy apply. This includes the mode assignment problem, selection rules, and the oscillator strength. In this work, the mode assignment problem was addressed with Finite Element calculations. These reveal that a rigid sphere in contact with a QCM displays two modes of vibration, termed “slipping” and “rocking”. In the slipping mode, the sphere rotates about its center; it exerts a tangential force onto the resonator surface at the point of contact. In the rocking mode, the sphere rotates about the point of contact; it exerts a torque onto the substrate. In liquids, both axes of rotation are slightly displaced from their ideal positions. Characteristic for spectroscopy, the two modes do not couple to the mechanical excitation equally well. The degree of coupling is quantified by an oscillator strength. Because the rocking mode mostly exerts a torque (rather than a tangential force, its coupling to the resonator's tangential motion is weak; the oscillator strength consequently is small. Recent experiments on surface-adsorbed colloidal spheres can be explained by the mode of vibration being of the rocking type. Keywords: Quartz crystal microbalance, Coupled resonance, Biocolloids, Adsorption

  12. Quartz-crystal microbalance study for characterizing atomic oxygen in plasma ash tools

    International Nuclear Information System (INIS)

    Srivastava, A.K.; Sakthivel, P.

    2001-01-01

    This article discusses the measurement of atomic oxygen (AO) concentrations in an oxygen discharge using a quartz-crystal microbalance (QCM). This is a device that has been previously used for monitoring thin-film deposition, among several other applications. The sensor consists of a silver-coated quartz crystal that oscillates at its specific resonant frequency (typically, at about 6 MHz), which is dependent on the mass of the crystal. When exposed to AO, the silver oxidizes rapidly, resulting in a change in its mass, and a consequent change in this frequency. The frequency change is measured with a counter, and when plotted versus time, it may be fit to a standard diffusion-limited oxide-growth model. This model is then used to determine the specific AO flux to the crystal, and by inference, to the wafer. Initial results of QCM measurements in the FusionGemini Plasma Asher (GPL TM -standard downstream microwave asher) and FusionGemini Enhanced Strip (GES TM -fluorine compatible enhanced strip asher) are presented in this article. The results indicate AO densities of the order of 10 12 cm -3 on the wafer. There is a marked increase in AO concentration with addition of nitrogen into the plasma, and a decrease in AO concentration with increasing pressure at constant flow. Effects of increasing the total plasma volume in the enhanced strip tool on AO production are discussed

  13. Low-cost scalable quartz crystal microbalance array for environmental sensing

    Energy Technology Data Exchange (ETDEWEB)

    Anazagasty, Cristain [University of Puerto Rico; Hianik, Tibor [Comenius University, Bratislava, Slovakia; Ivanov, Ilia N [ORNL

    2016-01-01

    Proliferation of environmental sensors for internet of things (IoT) applications has increased the need for low-cost platforms capable of accommodating multiple sensors. Quartz crystal microbalance (QCM) crystals coated with nanometer-thin sensor films are suitable for use in high-resolution (~1 ng) selective gas sensor applications. We demonstrate a scalable array for measuring frequency response of six QCM sensors controlled by low-cost Arduino microcontrollers and a USB multiplexer. Gas pulses and data acquisition were controlled by a LabVIEW user interface. We test the sensor array by measuring the frequency shift of crystals coated with different compositions of polymer composites based on poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS) while films are exposed to water vapor and oxygen inside a controlled environmental chamber. Our sensor array exhibits comparable performance to that of a commercial QCM system, while enabling high-throughput 6 QCM testing for under $1,000. We use deep neural network structures to process sensor response and demonstrate that the QCM array is suitable for gas sensing, environmental monitoring, and electronic-nose applications.

  14. In-Line Measurement of Water Content in Ethanol Using a PVA-Coated Quartz Crystal Microbalance

    Directory of Open Access Journals (Sweden)

    Byoung Chul Kim

    2014-01-01

    Full Text Available An in-line device for measuring the water content in ethanol was developed using a polyvinyl alcohol (PVA-coated quartz crystal microbalance. Bio-ethanol is widely used as the replacement of gasoline, and its water content is a key component of its specifications. When the PVA-coated quartz crystal microbalance is contacted with ethanol containing a small amount of water, the water is absorbed into the PVA increasing the load on the microbalance surface to cause a frequency drop. The determination performance of the PVA-coated microbalance is examined by measuring the frequency decreases in ethanol containing 2% to 10% water while the ethanol flows through the measurement device. The measurements indicates that the higher water content is the more the frequency reduction is, though some deviation in the measurements is observed. This indicates that the frequency measurement of an unknown concentration of water in ethanol can be used to determine the water content in ethanol. The PVA coating is examined by microscopy and FTIR (Fourier transform infrared spectroscopy.

  15. Use of the quartz crystal microbalance to determine the monomeric friction coefficient of polyimides

    Science.gov (United States)

    Bechtold, Mary M.

    1995-01-01

    When a thin film of polymer is coated on to a quartz crystal microbalance (QCM), the QCM can be used to detect the rate of increase in weight of the polymer film as the volatile penetrant diffuses into the polymer. From this rate information the diffusion coefficient of the penetrant into the polymer can be computed. Calculations requiring this diffusion coefficient lead to values which approximate the monomeric friction coefficient of the polymer. This project has been concerned with the trial of crystal oscillating circuits suitable for driving polymer coated crystals in an atmosphere of penetrant. For these studies done at room temperature, natural rubber was used as an easily applied polymer that is readily penetrated by toluene vapors, qualities anticipated with polyimides when they are tested at T(g) in the presence of toluene. Three quartz crystal oscillator circuits were tested. The simplest circuit used +/- 5 volt dc and had a transistor to transistor logic (TTL) inverter chip that provides a 180 deg phase shift via a feed back loop. This oscillator circuit was stable but would not drive the crystal when the crystal was coated with polymer and subjected to toluene vapors. Removal of a variable resistor from this circuit increased stability but did not otherwise increase performance. Another driver circuit tested contained a two stage differential input, differential output, wide band video amplifier and also contain a feed back loop. The circuit voltage could not be varied and operated at +/- 5 volts dc; this circuit was also stable but failed to oscillate the polymer coated crystal in an atmosphere saturated with toluene vapors. The third oscillator circuit was of similar construction and relied on the same video amplifier but allowed operation with variable voltage. This circuit would drive the crystal when the crystal was submerged in liquid toluene and when the crystal was coated with polymer and immersed in toluene vapors. The frequency readings

  16. Lectin typing of Campylobacter jejuni using a novel quartz crystal microbalance technique

    Energy Technology Data Exchange (ETDEWEB)

    Yakovleva, Maria E., E-mail: maria.yakovleva@gmail.com [Department of Infectious Diseases and Medical Microbiology, Lund University, 223 62 Lund (Sweden); Moran, Anthony P. [Department of Microbiology, School of Natural Sciences, National University of Ireland, Galway (Ireland); Safina, Gulnara R. [Department of Analytical and Marine Chemistry, University of Gothenburg, 412 96 Gothenburg (Sweden); Wadstroem, Torkel [Department of Infectious Diseases and Medical Microbiology, Lund University, 223 62 Lund (Sweden); Danielsson, Bengt [Acromed Invest AB, Magistratsvaegen 10, 226 43 Lund (Sweden)

    2011-05-23

    Seven Campylobacter jejuni strains were characterised by a lectin typing assay. The typing system was based on a quartz crystal microbalance technique (QCM) with four commercially available lectins (wheat germ agglutinin, Maackia amurensis lectin, Lens culinaris agglutinin, and Concanavalin A), which were chosen for their differing carbohydrate specificities. Initially, the gold surfaces of the quartz crystals were modified with 11-mercaptoundecanoic acid followed by lectin immobilisation using a conventional amine-coupling technique. Bacterial cells were applied for lectin typing without preliminary treatment, and resonant frequency and dissipation responses were recorded. The adhesion of microorganisms on lectin surfaces was confirmed by atomic force microscopy. Scanning was performed in the tapping mode and the presence of bacteria on lectin-coated surfaces was successfully demonstrated. A significant difference in the dissipation response was observed for different C. jejuni strains which made it possible to use this parameter for discriminating between bacterial strains. In summary, the QCM technique proved a powerful tool for the recognition and discrimination of C. jejuni strains. The approach may also prove applicable to strain discrimination of other bacterial species, particularly pathogens.

  17. Lectin typing of Campylobacter jejuni using a novel quartz crystal microbalance technique

    International Nuclear Information System (INIS)

    Yakovleva, Maria E.; Moran, Anthony P.; Safina, Gulnara R.; Wadstroem, Torkel; Danielsson, Bengt

    2011-01-01

    Seven Campylobacter jejuni strains were characterised by a lectin typing assay. The typing system was based on a quartz crystal microbalance technique (QCM) with four commercially available lectins (wheat germ agglutinin, Maackia amurensis lectin, Lens culinaris agglutinin, and Concanavalin A), which were chosen for their differing carbohydrate specificities. Initially, the gold surfaces of the quartz crystals were modified with 11-mercaptoundecanoic acid followed by lectin immobilisation using a conventional amine-coupling technique. Bacterial cells were applied for lectin typing without preliminary treatment, and resonant frequency and dissipation responses were recorded. The adhesion of microorganisms on lectin surfaces was confirmed by atomic force microscopy. Scanning was performed in the tapping mode and the presence of bacteria on lectin-coated surfaces was successfully demonstrated. A significant difference in the dissipation response was observed for different C. jejuni strains which made it possible to use this parameter for discriminating between bacterial strains. In summary, the QCM technique proved a powerful tool for the recognition and discrimination of C. jejuni strains. The approach may also prove applicable to strain discrimination of other bacterial species, particularly pathogens.

  18. Quartz Crystal Microbalance with Dissipation (QCM-D) studies of the viscoelastic response from a continuously growing grafted polyelectrolyte layer

    DEFF Research Database (Denmark)

    Dunér, Gunnar; Thormann, Esben; Dedinaite, Andra

    2013-01-01

    Poly(acrylic acid) was grown from substrates by photopolymerization, and the grafting process was monitored in situ by Quartz Crystal Microbalance with Dissipation (QCM-D) measurements in a 1:1 v/v mixture of water/ethanol. The polymerization process was monitored into the thick film region, wher...... that should be considered when investigating small changes in thick films used in e.g. sensor applications. © 2013 Elsevier Inc....

  19. Fundamental study on dissolution behavior of poly(methyl methacrylate) by quartz crystal microbalance

    Science.gov (United States)

    Konda, Akihiro; Yamamoto, Hiroki; Yoshitake, Shusuke; Kozawa, Takahiro

    2016-03-01

    Ionizing radiations such as extreme ultraviolet (EUV) and electron beam (EB) are the most promising exposure source for next-generation lithographic technology. In the realization of high resolution lithography, it is necessary for resist materials to improve the trade-off relationship among sensitivity, resolution, and line width roughness (LWR). In order to overcome them, it is essential to understand basic chemistry of resist matrices in resist processes. In particular, the dissolution process of resist materials is a key process. Therefore, it is essential for next-generation resist design for ionizing radiation to clarify the dissolution behavior of the resist film into developer. However, the details in dissolution process of EUV and EB resist films have not been investigated thus far. In this study, main chain scission and dissolution behavior of poly(methyl methacrylate) (PMMA) as main chain scission type resist was investigated using quartz crystal microbalance (QCM) method and gel permeation chromatography (GPC) in order to understand the relationship between the degree of PMMA degradation and dissolution behavior. The relationship between the molecular weight after irradiation and the swelling behavior was clarified.

  20. Study of quartz crystal microbalance NO2 sensor coated with sputtered indium tin oxide film

    Science.gov (United States)

    Georgieva, V.; Aleksandrova, M.; Stefanov, P.; Grechnikov, A.; Gadjanova, V.; Dilova, T.; Angelov, Ts

    2014-12-01

    A study of NO2 gas sorption ability of thin indium tin oxide (ITO) deposited on 16 MHz quartz crystal microbalance (QCM) is presented. ITO films are grown by RF sputtering of indium/tin target with weight proportion 95:5 in oxygen environment. The ITO films have been characterized by X-ray photoelectron spectroscopy measurements. The ITO surface composition in atomic % is defined to be: In-40.6%, Sn-4.3% and O-55%. The thickness and refractive index of the films are determined by ellipsometric method. The frequency shift of QCM-ITO is measured at different NO2 concentrations. The QCM-ITO system becomes sensitive at NO2 concentration >= 500 ppm. The sorbed mass for each concentration is calculated according the Sauerbrey equation. The results indicated that the 1.09 ng of the gas is sorbed into 150 nm thick ITO film at 500 ppm NO2 concentration. When the NO2 concentration increases 10 times the calculated loaded mass is 5.46 ng. The sorption process of the gas molecules is defined as reversible. The velocity of sorbtion /desorption processes are studied, too. The QCM coated with thin ITO films can be successfully used as gas sensors for detecting NO2 in the air at room temperature.

  1. Study of quartz crystal microbalance NO2 sensor coated with sputtered indium tin oxide film

    International Nuclear Information System (INIS)

    Georgieva, V; Gadjanova, V; Angelov, Ts; Aleksandrova, M; Acad. Georgi Bonchev str.bl. 11, 1113, Sofia (Bulgaria))" data-affiliation=" (Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Acad. Georgi Bonchev str.bl. 11, 1113, Sofia (Bulgaria))" >Stefanov, P; Acad. Georgi Bonchev str.bl. 11, 1113, Sofia (Bulgaria))" data-affiliation=" (Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Acad. Georgi Bonchev str.bl. 11, 1113, Sofia (Bulgaria))" >Dilova, T; Grechnikov, A

    2014-01-01

    A study of NO 2 gas sorption ability of thin indium tin oxide (ITO) deposited on 16 MHz quartz crystal microbalance (QCM) is presented. ITO films are grown by RF sputtering of indium/tin target with weight proportion 95:5 in oxygen environment. The ITO films have been characterized by X-ray photoelectron spectroscopy measurements. The ITO surface composition in atomic % is defined to be: In-40.6%, Sn-4.3% and O-55%. The thickness and refractive index of the films are determined by ellipsometric method. The frequency shift of QCM-ITO is measured at different NO 2 concentrations. The QCM-ITO system becomes sensitive at NO 2 concentration ≥ 500 ppm. The sorbed mass for each concentration is calculated according the Sauerbrey equation. The results indicated that the 1.09 ng of the gas is sorbed into 150 nm thick ITO film at 500 ppm NO 2 concentration. When the NO 2 concentration increases 10 times the calculated loaded mass is 5.46 ng. The sorption process of the gas molecules is defined as reversible. The velocity of sorbtion /desorption processes are studied, too. The QCM coated with thin ITO films can be successfully used as gas sensors for detecting NO 2 in the air at room temperature

  2. Quantifying Ion Transport in Polymers Using Electrochemical Quartz Crystal Microbalance with Dissipation

    Science.gov (United States)

    Lutkenhaus, Jodie; Wang, Shaoyang

    For polymers in energy systems, one of the most common means of quantifying ion transport is that of electrochemical impedance spectroscopy, in which an alternating electric field is applied and the resultant impedance response is recorded. While useful, this approach misses subtle details in transient film swelling, effects of hydration or solvent shells around the transporting ion, and changes in mechanical properties of the polymer. Here we present electrochemical quartz crystal microbalance with dissipation (EQCMD) monitoring as a means to quantify ion transport, dynamic swelling, and mechanical properties of polymers during electrochemical interrogation. We focus upon EQCMD characterization of the redox-active nitroxide radical polymer, poly(2,2,6,6-tetramethylpiperidinyloxy methacrylate) (PTMA). Upon oxidation, PTMA becomes positively charged, which requires the transport of a complementary anion into the polymer for electroneutrality. By EQCMD, we quantify anion transport and resultant swelling upon oxidation, as well as decoupling of contributions attributed to the ion and the solvent. We explore the effect of different lithium electrolyte salts in which each salt gives different charge storage and mass transport behavior. This is attributed to varied polymer-dopant and dopant-solvent interactions. The work was supported by the Grant DE-SC0014006 funded by the U.S. Department of Energy, Office of Science.

  3. Gold clusters sliding on graphite: a possible quartz crystal microbalance experiment?

    International Nuclear Information System (INIS)

    Pisov, S; Tosatti, E; Tartaglino, U; Vanossi, A

    2007-01-01

    A large measured two-dimensional (2D) diffusion coefficient of gold nanoclusters on graphite has been known experimentally and theoretically for about a decade. When subjected to a lateral force, these clusters should slide with an amount of friction that can be measured. We examine the hypothetical possibility of measuring by quartz crystal microbalance (QCM) the phononic sliding friction of gold clusters in the size range around 250 atoms on a graphite substrate between 300 and 600 K. Assuming the validity of Einstein's relations of ordinary Brownian motion and making use of the experimentally available activated behaviour of the diffusion coefficients, we can predict the sliding friction and slip times as a function of temperature. It is found that a prototypical deposited gold cluster could yield slip times at the standard measurable size of 10 -9 s for temperatures around 450-500 K, or 200 0 C. Since gold nanoclusters may also melt at around these temperatures, QCM could offer the additional chance of observing this phenomenon through a frictional change

  4. Scanning tunneling microscope-quartz crystal microbalance study of temperature gradients at an asperity contact.

    Science.gov (United States)

    Pan, L; Krim, J

    2013-01-01

    Investigations of atomic-scale friction frequently involve setups where a tip and substrate are initially at different temperatures. The temperature of the sliding interface upon contact has thus become a topic of interest. A method for detecting initial tip-sample temperature differences at an asperity contact is described, which consists of a scanning tunneling microscope (STM) tip in contact with the surface electrode of a quartz crystal microbalance (QCM). The technique makes use of the fact that a QCM is extremely sensitive to abrupt changes in temperature. In order to demonstrate the technique's capabilities, QCM frequency shifts were recorded for varying initial tip-substrate temperature differences as an STM tip was brought into and out of contact. The results are interpreted within the context of a recent model for thermal heat conduction at an asperity contact, and it is concluded that the transient frequency response is attributable to small changes in temperature close to the region of contact rather than a change in the overall temperature of the QCM itself. For the assumed model parameters, the results moreover reveal substantial temperature discontinuities at the boundary between the tip and the sample, for example, on the order of 10-15 °C for initial temperature differences of 20 °C.

  5. Transient effects during erosion of WN by deuterium ions studied with the quartz crystal microbalance technique

    Energy Technology Data Exchange (ETDEWEB)

    Berger, Bernhard M., E-mail: berger@iap.tuwien.ac.at [Institute of Applied Physics, TU Wien, Fusion@ÖAW, Wiedner Hauptstr. 8-10, 1040 Vienna (Austria); Stadlmayr, Reinhard [Institute of Applied Physics, TU Wien, Fusion@ÖAW, Wiedner Hauptstr. 8-10, 1040 Vienna (Austria); Meisl, Gerd [Max-Planck-Institut für Plasmaphysik, Boltzmannstraße 2, 85748 Garching (Germany); Čekada, Miha [Jožef Stefan Institute, Jamova 39, 1000 Ljubljana (Slovenia); Eisenmenger-Sittner, Christoph [Institute of Solid State Physics, TU Wien, Wiedner Hauptstr. 8-10, 1040 Vienna (Austria); Schwarz-Selinger, Thomas [Max-Planck-Institut für Plasmaphysik, Boltzmannstraße 2, 85748 Garching (Germany); Aumayr, Friedrich, E-mail: aumayr@iap.tuwien.ac.at [Institute of Applied Physics, TU Wien, Fusion@ÖAW, Wiedner Hauptstr. 8-10, 1040 Vienna (Austria)

    2016-09-01

    Transient effects during erosion of polycrystalline tungsten-nitride (WN) films by mono-energetic deuterium projectiles are studied using a quartz crystal microbalance technique. The evolution of the mass removal rate of a 360 nm thin WN film under 500 eV/D and 1000 eV/D bombardment is investigated at a temperature of 465 K in situ and in real-time as a function of the deuterium fluence. The measurements are performed at a typical flux of 10{sup 18} m{sup −2} s{sup −1}. A strong dependency of the observed mass change rate on the deuterium fluence is found. The mass loss is initially higher than for pure tungsten (W) and drops with fluence, finally reaching the same steady state value as for pure W sputtering. Steady state surface conditions are obtained at a fluence of about 0.2 × 10{sup 23} D/m{sup 2} for 500 eV/D and 0.6 × 10{sup 23} D/m{sup 2} for 1000 eV/D. SDTrimSP simulations indicate a preferential removal of N and a corresponding W enrichment of the surface.

  6. Protein Adsorption to Titanium and Zirconia Using a Quartz Crystal Microbalance Method

    Directory of Open Access Journals (Sweden)

    You Kusakawa

    2017-01-01

    Full Text Available Protein adsorption onto titanium (Ti or zirconia (ZrO2 was evaluated using a 27 MHz quartz crystal microbalance (QCM. As proteins, fibronectin (Fn, a cell adhesive protein, and albumin (Alb, a cell adhesion-inhibiting protein, were evaluated. The Ti and ZrO2 sensors for QCM were characterized by atomic force microscopy and electron probe microanalysis observation, measurement of contact angle against water, and surface roughness. The amounts of Fn and Alb adsorbed onto the Ti and ZrO2 sensors and apparent reaction rate were obtained using QCM measurements. Ti sensor showed greater adsorption of Fn and Alb than the ZrO2 sensor. In addition, amount of Fn adsorbed onto the Ti or ZrO2 sensors was higher than that of Alb. The surface roughness and hydrophilicity of Ti or ZrO2 may influence the adsorption of Fn or Alb. With regard to the adsorption rate, Alb adsorbed more rapidly than Fn onto Ti. Comparing Ti and ZrO2, Alb adsorption rate to Ti was faster than that to ZrO2. Fn adsorption will be effective for cell activities, but Alb adsorption will not. QCM method could simulate in vivo Fn and Alb adsorption to Ti or ZrO2.

  7. Quantitative analyses of Streptococcus mutans biofilms with quartz crystal microbalance, microjet impingement and confocal microscopy.

    Science.gov (United States)

    Kreth, J; Hagerman, E; Tam, K; Merritt, J; Wong, D T W; Wu, B M; Myung, N V; Shi, W; Qi, F

    2004-10-01

    Microbial biofilm formation can be influenced by many physiological and genetic factors. The conventional microtiter plate assay provides useful but limited information about biofilm formation. With the fast expansion of the biofilm research field, there are urgent needs for more informative techniques to quantify the major parameters of a biofilm, such as adhesive strength and total biomass. It would be even more ideal if these measurements could be conducted in a real-time, non-invasive manner. In this study, we used quartz crystal microbalance (QCM) and microjet impingement (MJI) to measure total biomass and adhesive strength, respectively, of S. mutans biofilms formed under different sucrose concentrations. In conjunction with confocal laser scanning microscopy (CLSM) and the COMSTAT software, we show that sucrose concentration affects the biofilm strength, total biomass, and architecture in both qualitative and quantitative manners. Our data correlate well with previous observations about the effect of sucrose on the adherence of S. mutans to the tooth surface, and demonstrate that QCM is a useful tool for studying the kinetics of biofilm formation in real time and that MJI is a sensitive, easy-to-use device to measure the adhesive strength of a biofilm.

  8. Biomimetic Receptors for Bioanalyte Detection by Quartz Crystal Microbalances — From Molecules to Cells

    Directory of Open Access Journals (Sweden)

    Usman Latif

    2014-12-01

    Full Text Available A universal label-free detection of bioanalytes can be performed with biomimetic quartz crystal microbalance (QCM coatings prepared by imprinting strategies. Bulk imprinting was used to detect the endocrine disrupting chemicals (EDCs known as estradiols. The estrogen 17β-estradiol is one of the most potent EDCs, even at very low concentrations. A highly sensitive, selective and robust QCM sensor was fabricated for real time monitoring of 17β-estradiol in water samples by using molecular imprinted polyurethane. Optimization of porogen (pyrene and cross-linker (phloroglucinol levels leads to improved sensitivity, selectivity and response time of the estradiol sensor. Surface imprinting of polyurethane as sensor coating also allowed us to generate interaction sites for the selective recognition of bacteria, even in a very complex mixture of interfering compounds, while they were growing from their spores in nutrient solution. A double molecular imprinting approach was followed to transfer the geometrical features of natural bacteria onto the synthetic polymer to generate biomimetic bacteria. The use of biomimetic bacteria as template makes it possible to prepare multiple sensor coatings with similar sensitivity and selectivity. Thus, cell typing, e.g., differentiation of bacteria strains, bacteria growth profile and extent of their nutrition, can be monitored by biomimetic mass sensors. Obviously, this leads to controlled cell growth in bioreactors.

  9. A hybrid humidity sensor using optical waveguides on a quartz crystal microbalance

    International Nuclear Information System (INIS)

    Shinbo, Kazunari; Otuki, Shunya; Kanbayashi, Yuichi; Ohdaira, Yasuo; Baba, Akira; Kato, Keizo; Kaneko, Futao; Miyadera, Nobuo

    2009-01-01

    In this study, slab and ridge optical waveguides (OWGs) made of fluorinated polyimides were deposited on a quartz crystal microbalance (QCM), and hybrid sensors using OWG spectroscopy and the QCM technique were prepared. Polyvinyl alcohol (PVA) film with CoCl 2 was deposited on the OWGs, and the characteristics of humidity sensing were investigated. A prism coupler was used to enter a He-Ne laser beam (λ = 632.8 nm) to the slab OWG. The output light intensity markedly changed due to chromism of the CoCl 2 as a result of humidity sorption, and this change was dependent on the incident angle of the laser beam to the slab OWG. During the measurement of output light, the QCM frequency was simultaneously monitored. The humidity dependence of the sensor with the slab OWG was also investigated in the range from 15 to 85%. For the sensor with the ridge OWG, white light was entered by butt-coupling, and the characteristics of humidity sensing were investigated by observing the output light spectrum and the QCM frequency.

  10. Frequency-shift vs phase-shift characterization of in-liquid quartz crystal microbalance applications

    International Nuclear Information System (INIS)

    Montagut, Y. J.; Garcia, J. V.; Jimenez, Y.; Arnau, A.; March, C.; Montoya, A.

    2011-01-01

    The improvement of sensitivity in quartz crystal microbalance (QCM) applications has been addressed in the last decades by increasing the sensor fundamental frequency, following the increment of the frequency/mass sensitivity with the square of frequency predicted by Sauerbrey. However, this sensitivity improvement has not been completely transferred in terms of resolution. The decrease of frequency stability due to the increase of the phase noise, particularly in oscillators, made impossible to reach the expected resolution. A new concept of sensor characterization at constant frequency has been recently proposed. The validation of the new concept is presented in this work. An immunosensor application for the detection of a low molecular weight contaminant, the insecticide carbaryl, has been chosen for the validation. An, in principle, improved version of a balanced-bridge oscillator is validated for its use in liquids, and applied for the frequency shift characterization of the QCM immunosensor application. The classical frequency shift characterization is compared with the new phase-shift characterization concept and system proposed.

  11. Adsorption of quantum dots onto polymer and Gemini surfactant films: a quartz crystal microbalance study.

    Science.gov (United States)

    Alejo, T; Merchán, M D; Velázquez, M M

    2014-08-26

    We used quartz crystal microbalance with dissipation to study the mechanical properties, the kinetics of adsorption, and the amount of CdSe quantum dots (QDs) adsorbed onto a SiO2 sensor, referred as bare sensor, onto the sensor modified with a film of the polymer poly(maleic anhydride-alt-1-octadecene), PMAO, or with a film of the Gemini surfactant ethyl-bis(dimethyl octadecyl ammonium bromide), abbreviated as 18-2-18. Results showed that when the sensor is coated with polymer or surfactant molecules, the coverage increases compared with that obtained for the bare sensor. On the other hand, rheological properties and kinetics of adsorption of QDs are driven by QD nanoparticles. Thus, the QD films present elastic behavior, and the elasticity values are independent of the molecule used as coating and similar to the elasticity value obtained for QDs films on the bare sensor. The QD adsorption is a two-step mechanism in which the fastest process is attributed to the QD adsorption onto the solid substrate and the slowest one is ascribed to rearrangement movements of the nanoparticles adsorbed at the surface.

  12. A Review of Interface Electronic Systems for AT-cut Quartz Crystal Microbalance Applications in Liquids.

    Science.gov (United States)

    Arnau, Antonio

    2008-01-21

    From the first applications of AT-cut quartz crystals as sensors in solutionsmore than 20 years ago, the so-called quartz crystal microbalance (QCM) sensor isbecoming into a good alternative analytical method in a great deal of applications such asbiosensors, analysis of biomolecular interactions, study of bacterial adhesion at specificinterfaces, pathogen and microorganism detection, study of polymer film-biomolecule orcell-substrate interactions, immunosensors and an extensive use in fluids and polymercharacterization and electrochemical applications among others. The appropriateevaluation of this analytical method requires recognizing the different steps involved andto be conscious of their importance and limitations. The first step involved in a QCMsystem is the accurate and appropriate characterization of the sensor in relation to thespecific application. The use of the piezoelectric sensor in contact with solutions stronglyaffects its behavior and appropriate electronic interfaces must be used for an adequatesensor characterization. Systems based on different principles and techniques have beenimplemented during the last 25 years. The interface selection for the specific application isimportant and its limitations must be known to be conscious of its suitability, and foravoiding the possible error propagation in the interpretation of results. This article presentsa comprehensive overview of the different techniques used for AT-cut quartz crystalmicrobalance in in-solution applications, which are based on the following principles:network or impedance analyzers, decay methods, oscillators and lock-in techniques. Theelectronic interfaces based on oscillators and phase-locked techniques are treated in detail,with the description of different configurations, since these techniques are the most used inapplications for detection of analytes in solutions, and in those where a fast sensorresponse is necessary.

  13. A Review of Interface Electronic Systems for AT-cut Quartz Crystal Microbalance Applications in Liquids

    Directory of Open Access Journals (Sweden)

    Antonio Arnau

    2008-01-01

    Full Text Available From the first applications of AT-cut quartz crystals as sensors in solutionsmore than 20 years ago, the so-called quartz crystal microbalance (QCM sensor isbecoming into a good alternative analytical method in a great deal of applications such asbiosensors, analysis of biomolecular interactions, study of bacterial adhesion at specificinterfaces, pathogen and microorganism detection, study of polymer film-biomolecule orcell-substrate interactions, immunosensors and an extensive use in fluids and polymercharacterization and electrochemical applications among others. The appropriateevaluation of this analytical method requires recognizing the different steps involved andto be conscious of their importance and limitations. The first step involved in a QCMsystem is the accurate and appropriate characterization of the sensor in relation to thespecific application. The use of the piezoelectric sensor in contact with solutions stronglyaffects its behavior and appropriate electronic interfaces must be used for an adequatesensor characterization. Systems based on different principles and techniques have beenimplemented during the last 25 years. The interface selection for the specific application isimportant and its limitations must be known to be conscious of its suitability, and foravoiding the possible error propagation in the interpretation of results. This article presentsa comprehensive overview of the different techniques used for AT-cut quartz crystalmicrobalance in in-solution applications, which are based on the following principles:network or impedance analyzers, decay methods, oscillators and lock-in techniques. Theelectronic interfaces based on oscillators and phase-locked techniques are treated in detail,with the description of different configurations, since these techniques are the most used inapplications for detection of analytes in solutions, and in those where a fast sensorresponse is necessary.

  14. Quantitative Rheometry of Thin Soft Materials Using the Quartz Crystal Microbalance with Dissipation.

    Science.gov (United States)

    Sadman, Kazi; Wiener, Clinton G; Weiss, R A; White, Christopher C; Shull, Kenneth R; Vogt, Bryan D

    2018-03-20

    In the inertial limit, the resonance frequency of the quartz crystal microbalance (QCM) is related to the coupled mass on the quartz sensor through the Sauerbrey expression that relates the mass to the change in resonance frequency. However, when the thickness of the film is sufficiently large, the relationship becomes more complicated and both the frequency and damping of the crystal resonance must be considered. In this regime, a rheological model of the material must be used to accurately extract the adhered film's thickness, shear modulus, and viscoelastic phase angle from the data. In the present work we examine the suitability of two viscoelastic models, a simple Voigt model ( Physica Scripta 1999, 59, 391-396) and a more realistic power-law model ( Langmuir 2015, 31, 4008-4017), to extract the rheological properties of a thermoresponsive hydrogel film. By changing temperature and initial dry film thickness of the gel, the operation of QCM was traversed from the Sauerbrey limit, where viscous losses do not impact the frequency, through the regime where the QCM response is sensitive to viscoelastic properties. The density-shear modulus and the viscoelastic phase angle from the two models are in good agreement when the shear wavelength ratio, d/λ n , is in the range of 0.05-0.20, where d is the film thickness and λ n is the wavelength of the mechanical shear wave at the n th harmonic. We further provide a framework for estimating the physical properties of soft materials in the megahertz regime by using the physical behavior of polyelectrolyte complexes. This provides the user with an approximate range of allowable film thicknesses for accurate viscoelastic analysis with either model, thus enabling better use of the QCM-D in soft materials research.

  15. Piezoelectric crystal microbalance measurements of enthalpy of sublimation of C2-C9 dicarboxylic acids

    Science.gov (United States)

    Dirri, F.; Palomba, E.; Longobardo, A.; Zampetti, E.

    2016-02-01

    We present here a novel experimental set-up that is able to measure the enthalpy of sublimation of a given compound by means of piezoelectric crystal microbalances (PCMs). The PCM sensors have already been used for space measurements, such as for the detection of organic and non-organic volatile species and refractory materials in planetary environments. In Earth atmospherics applications, PCMs can be also used to obtain some physical-chemical processes concerning the volatile organic compounds (VOCs) present in atmospheric environments. The experimental set-up has been developed and tested on dicarboxylic acids. In this work, a temperature-controlled effusion cell was used to sublimate VOC, creating a molecular flux that was collimated onto a cold PCM. The VOC recondensed onto the PCM quartz crystal, allowing the determination of the deposition rate. From the measurements of deposition rates, it has been possible to infer the enthalpy of sublimation of adipic acid, i.e. ΔHsub : 141.6 ± 0.8 kJ mol-1, succinic acid, i.e. 113.3 ± 1.3 kJ mol-1, oxalic acid, i.e. 62.5 ± 3.1 kJ mol-1, and azelaic acid, i.e. 124.2 ± 1.2 kJ mol-1. The results obtained show an accuracy of 1 % for succinic, adipic, and azelaic acid and within 5 % for oxalic acid and are in very good agreement with previous works (within 6 % for adipic, succinic, and oxalic acid and within 11 % or larger for azelaic acid).

  16. Hexamethyldisiloxane thin films as sensitive coating for quartz crystal microbalance based volatile organic compounds sensors

    International Nuclear Information System (INIS)

    Boutamine, M.; Bellel, A.; Sahli, S.; Segui, Y.; Raynaud, P.

    2014-01-01

    Hexamethyldisiloxane (HMDSO) thin films coated quartz crystal microbalance (QCM) electrodes have been characterized for the detection of volatile organic compounds (VOCs). The sensitive coatings were plasma polymerized in pure vapor of HMDSO and HMDSO/O 2 mixture. The sensor sensitivity was evaluated by monitoring the frequency shift (∆f) of the coated QCM electrode exposed to different concentrations of VOC vapors, such as ethanol, methanol, benzene and chloroform. The isotherm response characteristics showed good reproducibility and reversibility. For all types of analyte, ∆f were found to be linearly correlated with the concentration of VOC vapor. It was shown that it is possible to tune the chemical affinity of the sensor by changing the oxygen ratio in the deposition gas mixture. Contact angle measurements (CA), attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, atomic force microscopy (AFM) and scanning electron microscopy (SEM) were used to study surface wettability, chemical composition and surface morphology of the coated QCM electrodes. ATR-FTIR analysis showed the presence of methyl groups around 840 cm −1 due to Si-(CH 3 ) 3 rocking vibration making the elaborated sensor surface hydrophobic. When the coating is performed in HMDSO/O 2 mixture, AFM and SEM images showed an increase in the effective specific surface area of the sensor due to the increase in surface roughness. Surface morphology combined with chemical composition significantly affects the sensitivity of the QCM-based sensor. - Highlights: • Hexamethyldisiloxane layers were evaluated for volatile organic compounds detection. • The kinetic response of the sensor showed good reproducibility and reversibility. • Hydrophobic coating and high specific surface area increase the sensor sensitivity. • Sensor affinity can be controlled by controlling oxygen proportion in the mixture

  17. Measuring Enthalpy of Sublimation of Volatiles by Means of Piezoelectric Crystal Microbalances

    Science.gov (United States)

    Dirri, Fabrizio; Palomba, Ernesto; Longobardo, Andrea; Zampetti, Emiliano

    2017-12-01

    Piezoelectric Crystal Microbalances (PCM's) are widely used to study the chemical processes involving volatile compounds in any environment, such as condensation process. Since PCM's are miniaturized sensor, they are very suitable for planetary in situ missions, where can be used to detect and to measure the mass amount of astrobiologically significant compounds, such as water and organics. This work focuses on the realization and testing of a new experimental setup, able to characterize volatiles which can be found in a planetary environment. In particular the enthalpy of sublimation of some dicarboxylic acids has been measured. The importance of dicarboxylic acids in planetology and astrobiology is due to the fact that they have been detected in carbonaceous chondritic material (e.g. Murchinson), among the most pristine material present in our Solar System. In this work, a sample of acid was heated in an effusion cell up to its sublimation. For a set of temperatures (from 30 °C to 75 °C), the deposition rate on the PCM surface has been measured. From these measurements, it has been possible to infer the enthalpy of sublimation of Adipic acid, i.e. ΔH = 141.6 ± 0.8 kJ/mol and Succinic acid, i.e. ΔH = 113.3 ± 1.3 kJ/mol. This technique has so demonstrated to be a good choice to recognise a single compound or a mixture (with an analysis upstream) even if some improvements concerning the thermal stabilization of the system will be implemented in order to enhance the results' accuracy. The experiment has been performed in support of the VISTA (Volatile In Situ Thermogravimetry Analyzer) project, which is included in the scientific payload of the ESA MarcoPolo-R mission study.

  18. A different point of view on the sensitivity of quartz crystal microbalance sensors

    International Nuclear Information System (INIS)

    Arnau, Antonio; Montagut, Yeison; García, José V; Jiménez, Yolanda

    2009-01-01

    In this paper, the sensitivity of a quartz crystal microbalance (QCM) sensor is analysed and discussed in terms of the phase change versus the surface mass change, instead of the classical sensitivity in terms of the resonant frequency change derived from the well-known Sauerbrey equation. The detection sensitivity derived from the Sauerbrey equation is a theoretical detection capability in terms of the frequency change versus the mass change, which increases with the square of frequency. However, when a specific application and measuring system are considered, the detection capability of the QCM sensor must be considered from a different point of view. A new equation is obtained, Δψ ≅ −Δm c /(m q + m L ), which quantifies the phase shift, Δψ, of a fixed frequency signal corresponding to the series resonant frequency of the sensor in a reference state versus a change in the coating mass, Δm c ; m q = η q π/2v q , where η q is the loss viscosity of the unperturbed sensor and v q is the wave propagation speed in quartz, is a parameter which only depends on the physical parameters of the unperturbed resonator and fixes the maximum sensitivity of the sensor and m L = ρ L δ L /2, where ρ L and δ L are, respectively, the liquid density and the wave penetration depth of the wave in the liquid, is the equivalent surface mass density associated with the oscillatory movement of the surface of the sensor in contact with a fluid medium. This equation is an approximate equation around the series resonance frequency of the sensor. The simulation results for 10, 50 and 150 MHz resonance frequency QCM sensors probe its validity. A new electronic system is proposed for QCM biosensor applications based on the equation introduced

  19. Phase transition of pNIPAM grafted on plasma-activated PEO monitored in-situ by quartz crystal microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Heinz, P; Bretagnol, F; Mannelli, I; Gillil, D; Rauscher, H; Rossi, F [European Commission, Joint Research Centre, Institute for Health and Consumer Protection, 21020 Ispra (Vatican City State, Holy See,) (Italy)], E-mail: hubert.rauscher@jrc.it

    2008-03-15

    Thermoresponsive poly(N-isopropylacrylamide) layers were grafted on plasma-activated poly(ethylene oxide)-like substrate. Analysis by ToF-SIMS confirmed the presence of a pNIPAM film, which shows a phase transition temperature at 28 - 32 deg. C with hysteresis, as determined in-situ by quartz crystal microbalance. During the transition, the frequency of the pNIPAM coated quartz sensor exhibits a pronounced and unexpected minimum while the dissipation changes monotonously. This peculiar behaviour is explained by temporary formation of water-rich regions, which may cause delayed release and uptake of water during the collapse and re-swelling of the layer.

  20. Phase transition of pNIPAM grafted on plasma-activated PEO monitored in-situ by quartz crystal microbalance

    International Nuclear Information System (INIS)

    Heinz, P; Bretagnol, F; Mannelli, I; Gillil, D; Rauscher, H; Rossi, F

    2008-01-01

    Thermoresponsive poly(N-isopropylacrylamide) layers were grafted on plasma-activated poly(ethylene oxide)-like substrate. Analysis by ToF-SIMS confirmed the presence of a pNIPAM film, which shows a phase transition temperature at 28 - 32 deg. C with hysteresis, as determined in-situ by quartz crystal microbalance. During the transition, the frequency of the pNIPAM coated quartz sensor exhibits a pronounced and unexpected minimum while the dissipation changes monotonously. This peculiar behaviour is explained by temporary formation of water-rich regions, which may cause delayed release and uptake of water during the collapse and re-swelling of the layer

  1. A sensitive molecularly imprinted polymer based quartz crystal microbalance nanosensor for selective determination of lovastatin in red yeast rice.

    Science.gov (United States)

    Eren, Tanju; Atar, Necip; Yola, Mehmet Lütfi; Karimi-Maleh, Hassan

    2015-10-15

    Lovastatin (LOV) is a statin, used to lower cholesterol which has been found as a hypolipidemic agent in commercial red yeast rice. In present study, a sensitive molecular imprinted quartz crystal microbalance (QCM) sensor was prepared by fabricating a self-assembling monolayer formation of allylmercaptane on QCM chip surface for selective determination of lovastatin (LOV) in red yeast rice. To prepare molecular imprinted quartz crystal microbalance (QCM) nanosensor, LOV imprinted poly(2-hydroxyethyl methacrylate-methacryloylamidoaspartic acid) [p(HEMA-MAAsp)] nanofilm was attached on the modified gold surface of QCM chip. The non-modified and improved surfaces were characterized by using contact angle, atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy. The imprinted QCM sensor was validated according to the ICH guideline (International Conference on Harmonisation). The linearity range was obtained as 0.10-1.25 nM. The detection limit of the prepared material was calculated as 0.030 nM. The developed QCM nanosensor was successfully used to examine red yeast rice. Furthermore, the stability and repeatability of the prepared QCM nanosensor were studied. The spectacular long-term stability and repeatability of the prepared LOV-imprinted QCM nanosensor make them intriguing for use in QCM sensors. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Study on pivot-point vibration of molecular bond-rupture events by quartz crystal microbalance for biomedical diagnostics

    Directory of Open Access Journals (Sweden)

    Yuan YJ

    2012-01-01

    Full Text Available Yong J Yuan, Renjie JiaLaboratory of Biosensing and MicroMechatronics, School of Materials Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, People's Republic of ChinaAbstract: Bond-rupture scanning for biomedical diagnostics is examined using quartz crystal microbalance (QCM experiments and microparticle mechanics modeling calculations. Specific and nonspecific interactions between a microparticle and its binding QCM surface can be distinguished by gradually increasing the amplitude of driving voltage applied to QCM and monitoring its frequency changes. This research proposes a mechanical model of interactions between biological molecules and a QCM substrate surface. The mechanical force required to break a biotin–streptavidin bond was calculated through a one-pivot-point bottom-up vibration model. The bond-rupture force increases with an increase of the microparticle radius, the QCM resonant frequency, and the amplitude of driving voltage applied to the QCM. The significance of the research on biological molecular bond rupture is extremely important in characterizing microbial (such as cells and virus specificity, due to the force magnitude needed to break bonds using a transducer.Keywords: bond rupture, mechanical force, biomolecular binding energy spectra, quartz crystal microbalance (QCM

  3. Accurate dew-point measurement over a wide temperature range using a quartz crystal microbalance dew-point sensor

    Science.gov (United States)

    Kwon, Su-Yong; Kim, Jong-Chul; Choi, Buyng-Il

    2008-11-01

    Quartz crystal microbalance (QCM) dew-point sensors are based on frequency measurement, and so have fast response time, high sensitivity and high accuracy. Recently, we have reported that they have the very convenient attribute of being able to distinguish between supercooled dew and frost from a single scan through the resonant frequency of the quartz resonator as a function of the temperature. In addition to these advantages, by using three different types of heat sinks, we have developed a QCM dew/frost-point sensor with a very wide working temperature range (-90 °C to 15 °C). The temperature of the quartz surface can be obtained effectively by measuring the temperature of the quartz crystal holder and using temperature compensation curves (which showed a high level of repeatability and reproducibility). The measured dew/frost points showed very good agreement with reference values and were within ±0.1 °C over the whole temperature range.

  4. SHORT COMMUNICATION: Recognition of supercooled dew in a quartz crystal microbalance dew-point sensor by slip phenomena

    Science.gov (United States)

    Kwon, Su-Yong; Kim, Jong-Chul; Choi, Byung-Il

    2007-10-01

    Distinguishing between a supercooled dew and frost below 0 °C in dew/frost-point measurements is an important and challenging problem that has not yet been completely solved. This study presents a new method for the recognition of a supercooled dew in a dew/frost-point sensor. A quartz crystal microbalance (QCM) sensor was used as a dew/frost-point sensor to detect a dew and a supercooled dew as well as frost. The slip phenomenon occurring at an interface between the water droplet and the surface of the quartz crystal resonator of the QCM sensor gives a simple and accurate way of distinguishing between a supercooled dew and frost below 0 °C. This method can give a highly accurate measurement of the dew or the frost point without misreading in the dew-point sensor at temperatures below 0 °C.

  5. Improved electronic interfaces for AT-cut quartz crystal microbalance sensors under variable damping and parallel capacitance conditions.

    Science.gov (United States)

    Arnau, A; García, J V; Jimenez, Y; Ferrari, V; Ferrari, M

    2008-07-01

    A new configuration of automatic capacitance compensation (ACC) technique based on an oscillatorlike working interface, which permits the tracking of the series resonant frequency and the monitoring of the motional resistance and the parallel capacitance of a thickness-shear mode quartz crystal microbalance sensor, is introduced. The new configuration permits an easier calibration of the system which, in principle, improves the accuracy. Experimental results are reported with 9 and 10 MHz crystals in liquids with different parallel capacitances which demonstrate the effectiveness of the capacitance compensation. Some frequency deviations from the exact series resonant frequency, measured by an impedance analyzer, are explained by the specific nonideal behavior of the circuit components. A tentative approach is proposed to solve this problem that is also common to previous ACC systems.

  6. Improved electronic interfaces for AT-cut quartz crystal microbalance sensors under variable damping and parallel capacitance conditions

    International Nuclear Information System (INIS)

    Arnau, A.; Garcia, J. V.; Jimenez, Y.; Ferrari, V.; Ferrari, M.

    2008-01-01

    A new configuration of automatic capacitance compensation (ACC) technique based on an oscillatorlike working interface, which permits the tracking of the series resonant frequency and the monitoring of the motional resistance and the parallel capacitance of a thickness-shear mode quartz crystal microbalance sensor, is introduced. The new configuration permits an easier calibration of the system which, in principle, improves the accuracy. Experimental results are reported with 9 and 10 MHz crystals in liquids with different parallel capacitances which demonstrate the effectiveness of the capacitance compensation. Some frequency deviations from the exact series resonant frequency, measured by an impedance analyzer, are explained by the specific nonideal behavior of the circuit components. A tentative approach is proposed to solve this problem that is also common to previous ACC systems

  7. Mucoadhesion vs mucus permeability of thiolated chitosan polymers and their resulting nanoparticles using a quartz crystal microbalance with dissipation (QCM-D).

    Science.gov (United States)

    Oh, Sejin; Borrós, Salvador

    2016-11-01

    The aim of this present study was to evaluate the combination properties between mucoadhesion/mucus permeability of thiolated chitosans (TC) and their resulting nanoparticles using a quartz crystal microbalance with dissipation (QCM-D). The QCM-D experiments were conducted at pH 4 or 6.8 to assess the interaction between thiolated polymers, with low (TCL), medium (TCM) and high (TCH) contents of free thiol groups, and native porcine gastric mucin (NPGM). TCL was chosen for further carriers as it showed higher permeability into the NPGM layer compared to TCM and TCH. In this study, we describe a formulation of a novel carrier comprised by positively charged TCL, negatively charged DNA and degradable oligopeptide-modified poly(β-amino ester)s (PBAEs), which were employed in order to approach for tuning particle size and surface charge of complexes. TCL/PBAE complexes with or without DNA were characterized using dynamic light scattering. Mechanism of adsorption or permeation of the TCL/PBAE/DNA complexes into the NPGM barrier was investigated with QCM-D, which is a highly sensitive technique for studying nanomechanical (viscoelastic) changes of the substrates. This work might provide that the QCM-D technique would be a promising method to monitor the dynamic behaviour between complexes and NPGM. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Adsorption effectiveness of β-lactoglobulin onto gold surface determined by quartz crystal microbalance.

    Science.gov (United States)

    Jachimska, B; Świątek, S; Loch, J I; Lewiński, K; Luxbacher, T

    2018-06-01

    Bovine β-lactoglobulin (LGB) is a transport protein that can bind to its structure hydrophobic bioactive molecules. Due to the lack of toxicity, high stability and pH-dependent molecular binding mechanism, lactoglobulin can be used as a carrier of sparingly soluble drugs. Dynamic light scattering has confirmed LGB's tendency to create oligomeric forms. The hydrodynamic diameter of LGB molecules varies from 4 nm to 6 nm in the pH range of 2-10 and ionic strength I = 0.001-0.15 M, which corresponds to the presence of mono or dimeric LGB forms. The LGB zeta potential varies from 26.5 mV to -33.3 mV for I = 0.01 M and from 13.3 mV to -16 mV for I = 0.15 M in the pH range of 2-10. The isoelectric point is at pH 4.8. As a result of strong surface charge compensation, the maximum effective ionization degree of the LGB molecule is 35% for ionic strength I = 0.01 M and 22% for I = 0.15 M. The effectiveness of adsorption is linked with the properties of the protein, as well as those of the adsorption surface. The functionalization of gold surfaces with β-lactoglobulin (LGB) was studied using a quartz crystal microbalance with energy dissipation monitoring (QCM-D). The effectiveness of LGB adsorption correlates strongly with a charge of gold surface and the zeta potential of the molecule. The greatest value of the adsorbed mass was observed in the pH range in which LGB has a positive zeta potential values, below pH 4.8. This observation shows that electrostatic interactions play a dominant role in LGB adsorption on gold surfaces. Based on the adsorbed mass, protein orientation on gold surfaces was determined. The preferential side-on orientation of LGB molecules observed in the adsorption layer is consistent with the direction of the molecule dipole momentum determined by molecular dynamics simulations of the protein (MD). The use of the QCM-D method also allowed us to determine the effectiveness of adsorption of LGB on gold

  9. Measurement of the Ru surface content of electrodeposited PtRu electrodes with the electrochemical quartz crystal microbalance: implications for methanol and CO electrooxidation

    NARCIS (Netherlands)

    Frelink, T.; Visscher, W.; Veen, van J.A.R.

    1996-01-01

    To obtain the surface content of Ru in rough electrocodeposited PtRu electrodes, the mass change of a Pt electrode during Ru deposition was measured with the electrochemical quartz crystal microbalance (EQCMB). It is shown that there is a correlation between the potential of the surface oxide

  10. Study on pivot-point vibration of molecular bond-rupture events by quartz crystal microbalance for biomedical diagnostics.

    Science.gov (United States)

    Yuan, Yong J; Jia, Renjie

    2012-01-01

    Bond-rupture scanning for biomedical diagnostics is examined using quartz crystal microbalance (QCM) experiments and microparticle mechanics modeling calculations. Specific and nonspecific interactions between a microparticle and its binding QCM surface can be distinguished by gradually increasing the amplitude of driving voltage applied to QCM and monitoring its frequency changes. This research proposes a mechanical model of interactions between biological molecules and a QCM substrate surface. The mechanical force required to break a biotin-streptavidin bond was calculated through a one-pivot-point bottom-up vibration model. The bond-rupture force increases with an increase of the microparticle radius, the QCM resonant frequency, and the amplitude of driving voltage applied to the QCM. The significance of the research on biological molecular bond rupture is extremely important in characterizing microbial (such as cells and virus) specificity, due to the force magnitude needed to break bonds using a transducer.

  11. Determination of thermodynamic parameters for enolization reaction of malonic and metylmalonic acids by using quartz crystal microbalance

    Directory of Open Access Journals (Sweden)

    Minoru Yoshimoto

    2016-06-01

    Full Text Available We investigated the process of a bromination reaction of malonic acid and methylmalonic acid in the Belousov-Zhabotinsky reaction by using a quartz crystal microbalance (QCM. The process involves an enolization reaction as a rate-determining step. We found that, in the step, the variation of Br2 concentration induced an exactly quantitative shift of a resonant frequency of the QCM, based on the change of the surface mass on the QCM and the solution viscosity and density. This new finding enabled us to estimate the reaction rate constants and the thermodynamic parameters of the enolization reaction due to a QCM measurement. The values measured by the QCM were in good agreement with those measured by a UV-spectrophotometer. As a result, we succeeded to develop a new measurement method of a nonlinear chemical reaction.

  12. Real-time mass measurement of dust particles deposited on vessel wall in a divertor simulator using quartz crystal microbalances

    International Nuclear Information System (INIS)

    Tateishi, Mizuki; Koga, Kazunori; Katayama, Ryu; Yamashita, Daisuke; Kamataki, Kunihiro; Seo, Hyunwoong; Itagaki, Naho; Shiratani, Masaharu; Ashikawa, Naoko; Masuzaki, Suguru; Nishimura, Kiyohiko; Sagara, Akio

    2015-01-01

    We are developing a dust monitoring method using quartz crystal microbalances (QCMs) equipped with a dust eliminating filter. Here we report a dust eliminating ratio of the filter and first measurement results of the QCMs in a divertor simulator. The volume of spherical dust in unit area on the filter and QCM under the filter were 2.09 × 10 −9 and 1.22 × 10 −10 m 3 m −2 , respectively. Thus, the dust eliminating ratio of the filter is 94.2%. The QCM without the filter gives deposition rate due to radicals and dust particles, whereas the QCM with the filter gives deposition rate predominantly due to radicals. From the results, we deduce information of mass fraction of dust particles in deposits

  13. Establishing linear solvation energy relationships between VOCs and monolayer-protected gold nanoclusters using quartz crystal microbalance.

    Science.gov (United States)

    Li, Chi-Lin; Lu, Chia-Jung

    2009-08-15

    Linear solvation energy relationships (LSERs) have been recognized as a useful model for investigating the chemical forces behind the partition coefficients between vapor molecules and absorbents. This study is the first to determine the solvation properties of monolayer-protected gold nanoclusters (MPCs) with different surface ligands. The ratio of partition coefficients/MPC density (K/rho) of 18 volatile organic compounds (VOCs) for four different MPCs obtained through quartz crystal microbalance (QCM) experiments were used for the LSER model calculations. LSER modeling results indicate that all MPC surfaces showed a statistically significant (pattraction, 4-methoxythiophenol-capped MPCs can also interact with polar organics (s=1.04). Showing a unique preference for the hydrogen bond basicity of vapors (b=1.11), 2-benzothiazolethiol-capped MPCs provide evidence of an intra-molecular, proton-shift mechanism on surface of nano-gold.

  14. In-Line Measurement of Water Contents in Ethanol Using a Zeolite-Coated Quartz Crystal Microbalance

    Directory of Open Access Journals (Sweden)

    Byoung Chul Kim

    2015-10-01

    Full Text Available A quartz crystal microbalance (QCM was utilized to measure the water content in ethanol. For the improvement of measurement sensitivity, the QCM was modified by applying zeolite particles on the surface with poly(methyl methacrylate (PMMA binder. The measurement performance was examined with ethanol of 1% to 5% water content in circulation. The experimental results showed that the frequency drop of the QCM was related with the water content though there was some deviation. The sensitivity of the zeolite-coated QCM was sufficient to be implemented in water content determination, and a higher ratio of silicon to aluminum in the molecular structure of the zeolite gave better performance. The coated surface was inspected by microscopy to show the distribution of zeolite particles and PMMA spread.

  15. Effective antibodies immobilization and functionalized nanoparticles in a quartz-crystal microbalance-based immunosensor for the detection of parathion.

    Directory of Open Access Journals (Sweden)

    Bartolomeo Della Ventura

    Full Text Available Biosensor-based detection provides a rapid and low-cost alternative to conventional analytical methods for revealing the presence of the contaminants in water as well as solid matrices. Although important to be detected, small analytes (few hundreds of Daltons are an issue in biosensing since the signal they induce in the transducer, and specifically in a Quartz-Crystal Microbalance, is undetectable. A pesticide like parathion (M = 292 Da is a typical example of contaminant for which a signal amplification procedure is desirable.The ballasting of the analyte by gold nanoparticles has been already applied to heavy target as proteins or bacteria to improve the limit of detection. In this paper, we extend the application of such a method to small analytes by showing that once the working surface of a Quartz-Crystal Microbalance (QCM has been properly functionalized, a limit of detection lower than 1 ppb is reached for parathion. The effective surface functionalization is achieved by immobilizing antibodies upright oriented on the QCM gold surface by a simple photochemical technique (Photonic Immobilization Technique, PIT based on the UV irradiation of the antibodies, whereas a simple protocol provided by the manufacturer is applied to functionalize the gold nanoparticles. Thus, in a non-competitive approach, the small analyte is made detectable by weighing it down through a "sandwich protocol" with a second antibody tethered to heavy gold nanoparticles. The immunosensor has been proved to be effective against the parathion while showing no cross reaction when a mixture of compounds very similar to parathion is analyzed.The immunosensor described in this paper can be easily applied to any small molecule for which polyclonal antibodies are available since both the functionalization procedure of the QCM probe surface and gold nanoparticle can be applied to any IgG, thereby making our device of general application in terms of target analyte.

  16. The use of quartz crystal microbalance with dissipation (QCM-D for studying nanoparticle-induced platelet aggregation

    Directory of Open Access Journals (Sweden)

    Santos-Martinez MJ

    2012-01-01

    Full Text Available Maria Jose Santos-Martinez1–3, Iwona Inkielewicz-Stepniak1,4, Carlos Medina1, Kamil Rahme5,6, Deirdre M D'Arcy1, Daniel Fox3, Justin D Holmes3,5, Hongzhou Zhang3, Marek Witold Radomski3,51School of Pharmacy and Pharmaceutical Sciences, 2School of Medicine, 3Center for Research on Adaptive Nanostructures and Nanodevices, Trinity College Dublin, Dublin, Ireland; 4Department of Medicinal Chemistry, Medical University of Gdansk, Gdansk, Poland; 5Materials and Supercritical Fluids Group, Department of Chemistry and the Tyndall National Institute, University College Cork, Cork, Ireland; 6Department of Sciences, Faculty of Natural and Applied Science, Notre Dame University, Zouk Mosbeh, LebanonAbstract: Interactions between blood platelets and nanoparticles have both pharmacological and toxicological significance and may lead to platelet activation and aggregation. Platelet aggregation is usually studied using light aggregometer that neither mimics the conditions found in human microvasculature nor detects microaggregates. A new method for the measurement of platelet microaggregation under flow conditions using a commercially available quartz crystal microbalance with dissipation (QCM-D has recently been developed. The aim of the current study was to investigate if QCM-D could be used for the measurement of nanoparticle-platelet interactions. Silica, polystyrene, and gold nanoparticles were tested. The interactions were also studied using light aggregometry and flow cytometry, which measured surface abundance of platelet receptors. Platelet activation was imaged using phase contrast and scanning helium ion microscopy. QCM-D was able to measure nanoparticle-induced platelet microaggregation for all nanoparticles tested at concentrations that were undetectable by light aggregometry and flow cytometry. Microaggregates were measured by changes in frequency and dissipation, and the presence of platelets on the sensor surface was confirmed and imaged by

  17. Accurate dew-point measurement over a wide temperature range using a quartz crystal microbalance dew-point sensor

    International Nuclear Information System (INIS)

    Kwon, Su-Yong; Kim, Jong-Chul; Choi, Buyng-Il

    2008-01-01

    Quartz crystal microbalance (QCM) dew-point sensors are based on frequency measurement, and so have fast response time, high sensitivity and high accuracy. Recently, we have reported that they have the very convenient attribute of being able to distinguish between supercooled dew and frost from a single scan through the resonant frequency of the quartz resonator as a function of the temperature. In addition to these advantages, by using three different types of heat sinks, we have developed a QCM dew/frost-point sensor with a very wide working temperature range (−90 °C to 15 °C). The temperature of the quartz surface can be obtained effectively by measuring the temperature of the quartz crystal holder and using temperature compensation curves (which showed a high level of repeatability and reproducibility). The measured dew/frost points showed very good agreement with reference values and were within ±0.1 °C over the whole temperature range

  18. Adsorption Device Based on a Langatate Crystal Microbalance for High Temperature High Pressure Gas Adsorption in Zeolite H-ZSM-5.

    Science.gov (United States)

    Ding, Wenjin; Baracchini, Giulia; Klumpp, Michael; Schwieger, Wilhelm; Dittmeyer, Roland

    2016-08-25

    We present a high-temperature and high-pressure gas adsorption measurement device based on a high-frequency oscillating microbalance (5 MHz langatate crystal microbalance, LCM) and its use for gas adsorption measurements in zeolite H-ZSM-5. Prior to the adsorption measurements, zeolite H-ZSM-5 crystals were synthesized on the gold electrode in the center of the LCM, without covering the connection points of the gold electrodes to the oscillator, by the steam-assisted crystallization (SAC) method, so that the zeolite crystals remain attached to the oscillating microbalance while keeping good electroconductivity of the LCM during the adsorption measurements. Compared to a conventional quartz crystal microbalance (QCM) which is limited to temperatures below 80 °C, the LCM can realize the adsorption measurements in principle at temperatures as high as 200-300 °C (i.e., at or close to the reaction temperature of the target application of one-stage DME synthesis from the synthesis gas), owing to the absence of crystalline-phase transitions up to its melting point (1,470 °C). The system was applied to investigate the adsorption of CO2, H2O, methanol and dimethyl ether (DME), each in the gas phase, on zeolite H-ZSM-5 in the temperature and pressure range of 50-150 °C and 0-18 bar, respectively. The results showed that the adsorption isotherms of these gases in H-ZSM-5 can be well fitted by Langmuir-type adsorption isotherms. Furthermore, the determined adsorption parameters, i.e., adsorption capacities, adsorption enthalpies, and adsorption entropies, compare well to literature data. In this work, the results for CO2 are shown as an example.

  19. Superior environment resistance of quartz crystal microbalance with anatase TiO2/ZnO nanorod composite films

    International Nuclear Information System (INIS)

    Qiang, Wei; Wei, Li; Shaodan, Wang; Yu, Bai

    2015-01-01

    Graphical abstract: ZnO nanorod array being prepared by an in situ method on the QCM coated with Au film via hydrothermal process and surface modification with coated TiO 2 by sol–gel methods to form a superhydrophobic TiO 2 /ZnO composite film the anatase TiO 2 /ZnO nanorod composite film with a sharp, pencil-like structure exhibiting excellent superhydrophobicity (water contact angle of 155°), non-sticking water properties, and an autonomous cleaning property under UV irradiation. The anatase TiO 2 /ZnO nanorod composite film facilitates the precise measurement and extended lifetime of the QCM for the detection of organic gas molecules. - Highlights: • This work combines, for the first time, the advantage of the TiO 2 /ZnO composite film on photocatalysis and reversible super-hydrophobic and super-hydrophilic transition, and puts forward a solution to satisfy weatherability of quartz crystal microbalance in long-term application. • The anatase TiO 2 /ZnO nanorod composite film with pencil structure exhibit excellent super-hydrophobicity (water contact angle can reach 155°), no-sticking water properties and self-cleaning property under UV irradiation. • The photocatalysis and reversible super-hydrophobic and super-hydrophilic transition of the TiO 2 /ZnO nanorod composite film is stable in long-term application. - Abstract: The precise measurement of quartz crystal microbalance (QCM) in the detection and weighing of organic gas molecules is achieved due to excellent superhydrophobicity of a deposited film composite. Photocatalysis is utilized as a method for the self-cleaning of organic molecules on the QCM for extended long-term stability in the precision of the instrument. In this paper, ZnO nanorod array is prepared via in situ methods on the QCM coated with Au film via hydrothermal process. Subsequently, a TiO 2 /ZnO composite film is synthesized by surface modification with TiO 2 via sol–gel methods. Results show the anatase TiO 2 /ZnO nanorod

  20. Assessing the adsorption selectivity of linker functionalized, moisture-stable metal-organic framework thin films by means of an environment-controlled quartz crystal microbalance.

    Science.gov (United States)

    Bétard, Angélique; Wannapaiboon, Suttipong; Fischer, Roland A

    2012-11-04

    The stepwise thin film deposition of the robust, hydrophobic [Zn(4)O(dmcapz)(3)](n) (dmcapz = 3,5-dimethyl-4-carboxy-pyrazolato) is reported. The adsorption of small organic probe molecules, including alkanols, toluene, aniline and xylenes, was monitored by an environment-controlled quartz crystal microbalance setup. The adsorption selectivity was tuned by introducing alkyl side chains in the dmcapz linker.

  1. Polyacrylonitrile nanofiber as polar solvent N,N-dimethyl formamide sensor based on quartz crystal microbalance technique

    Science.gov (United States)

    Rianjanu, A.; Julian, T.; Hidayat, S. N.; Suyono, E. A.; Kusumaatmaja, A.; Triyana, K.

    2018-04-01

    Here, we describe an N,N-dimethyl formamide (DMF) vapour sensor fabricated by coating polyacrylonitrile (PAN) nanofiber structured on quartz crystal microbalance (QCM). The PAN nanofiber sensors with an average diameter of 225 nm to 310 nm were fabricated via electrospinning process with different mass deposition on QCM substrate. The nanostructured of PAN nanofiber offers a high specific surface area that improved the sensing performance of nanofiber sensors. Benefiting from that fine structure, and high polymer-solvent affinity between PAN and DMF, the development of DMF sensors presented good response at ambient temperature. Since there is no chemical reaction between PAN nanofiber and DMF vapour, weak physical interaction such absorption and swelling were responsible for the sensing behavior. The results are indicating that the response of PAN nanofiber sensors has more dependency on the nanofiber structure (specific surface area) rather than its mass deposition. The sensor also showed good stability after a few days sensing. These findings have significant implications for developing DMF vapour sensor based on QCM coated polymer nanofibers.

  2. In situ NMR and electrochemical quartz crystal microbalance techniques reveal the structure of the electrical double layer in supercapacitors

    Science.gov (United States)

    Griffin, John M.; Forse, Alexander C.; Tsai, Wan-Yu; Taberna, Pierre-Louis; Simon, Patrice; Grey, Clare P.

    2015-08-01

    Supercapacitors store charge through the electrosorption of ions on microporous electrodes. Despite major efforts to understand this phenomenon, a molecular-level picture of the electrical double layer in working devices is still lacking as few techniques can selectively observe the ionic species at the electrode/electrolyte interface. Here, we use in situ NMR to directly quantify the populations of anionic and cationic species within a working microporous carbon supercapacitor electrode. Our results show that charge storage mechanisms are different for positively and negatively polarized electrodes for the electrolyte tetraethylphosphonium tetrafluoroborate in acetonitrile; for positive polarization charging proceeds by exchange of the cations for anions, whereas for negative polarization, cation adsorption dominates. In situ electrochemical quartz crystal microbalance measurements support the NMR results and indicate that adsorbed ions are only partially solvated. These results provide new molecular-level insight, with the methodology offering exciting possibilities for the study of pore/ion size, desolvation and other effects on charge storage in supercapacitors.

  3. Development of a Quartz Crystal Microbalance Sensor Modified by Nano-Structured Polyaniline for Detecting the Plasticizer in Gaseous State

    Directory of Open Access Journals (Sweden)

    Hui XU

    2014-01-01

    Full Text Available A quartz crystal microbalance (QCM modified by a film of nano-structured polyaniline (nano-PANI is developed as a gas sensor for detecting the presence of the plasticizer, such as dibutyl phthalate (DBP in the ambient. Nano-PANI is prepared using a non-template method and the films are deposited using physical coating method. Scanning electron microscopy is used to characterize the nano-PANI film. The sensor response towards DBP is tested in a sealed gas chamber. The QCM resonant frequency shift is measured due to the absorption of DBP with different concentration ranging from 0.04 to 1.2 ppm. The experiment results show that the variation of the frequency is a linear function of DBP concentration and the sensitivity up to 54 Hz/ppm could be achieved by using the researched nano-PANI on QCM. To investigate the selectivity, the potential interfering analytes such as acetone, ethanol, acetaldehyde and formaldehyde are tested. And the mechanism hypothesis of the nano-PANI sensitive to the plasticizer is analyzed.

  4. Determination of functionalized gold nanoparticles incorporated in hydrophilic and hydrophobic microenvironments by surface modification of quartz crystal microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Tsui-Hsun [Institute of Biomedical Engineering, College of Engineering, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC (China); Institute of Medical Mechatronics, Chang Gung University, Tao-Yuan, Taiwan, ROC (China); Liao, Shu-Chuan [Center of Thin Film Technologies and Applications, Mingchi University of Technology, Taipei, Taiwan, ROC (China); Chen, Ying-Fang [Department of Dentistry, Yun-Lin Branch, National Taiwan University Hospital, Dou-Liu, Yun-Lin, Taiwan, ROC (China); Huang, Yi-You [Institute of Biomedical Engineering, College of Engineering, College of Medicine, National Taiwan University, Taipei, Taiwan, ROC (China); Wei, Yi-Syuan [Department of Materials Engineering, Tatung University, 40 Zhongshan North Road, 3rd Section, Taipei 104, Taiwan, ROC (China); Tu, Shu-Ju, E-mail: sjt@cgu.edu.tw [Department of Medical Imaging and Radiological Sciences, Chang Gung University, 259 Wen-Hwa, 1st Road, Kwei-Shan, Tao-Yuan 133, Taiwan, ROC (China); Chen, Ko-Shao, E-mail: kschen@ttu.edu.tw [Department of Materials Engineering, Tatung University, 40 Zhongshan North Road, 3rd Section, Taipei 104, Taiwan, ROC (China)

    2013-06-01

    In this study, plasma deposition methods were used to immobilize Au electrode of a quartz crystal microbalance (QCM) to create different microenvironments for mass measurement of various modified Au nanoparticles (AuNPs). AuNPs were modified by 11-mercaptoundecanoic acid (MUA) and 1-decanethiol (DCT) for potential applications to drug release, protective coatings, and immunosensors. We aimed to develop a highly sensitive and reliable method to quantify the mass of various modified AuNPs. The surface of AuNPs and Au electrode was coated with polymer films, as determined by Fourier transform infrared spectroscopy and atomic force microscopy. Measurements obtained for various AuNPs and the plasma-treated surface of the Au electrode were compared with those obtained for an untreated Au electrode. According to the resonant frequency shift of QCM, a linear relationship was observed that significantly differed for AuNPs, MUA-AuNPs, and DCT-AuNPs (R{sup 2} range, 0.94–0.965, 0.934–0.972, and 0.874–0.9514, respectively). Compared to inductively coupled plasma and micro-computerized tomography, the QCM method with plasma treatment has advantages of real-time monitoring, greater sensitivity, and lower cost. Our results demonstrate that surface modifications measured by a QCM system for various modified AuNPs were reliable.

  5. Determination of functionalized gold nanoparticles incorporated in hydrophilic and hydrophobic microenvironments by surface modification of quartz crystal microbalance

    International Nuclear Information System (INIS)

    Wu, Tsui-Hsun; Liao, Shu-Chuan; Chen, Ying-Fang; Huang, Yi-You; Wei, Yi-Syuan; Tu, Shu-Ju; Chen, Ko-Shao

    2013-01-01

    In this study, plasma deposition methods were used to immobilize Au electrode of a quartz crystal microbalance (QCM) to create different microenvironments for mass measurement of various modified Au nanoparticles (AuNPs). AuNPs were modified by 11-mercaptoundecanoic acid (MUA) and 1-decanethiol (DCT) for potential applications to drug release, protective coatings, and immunosensors. We aimed to develop a highly sensitive and reliable method to quantify the mass of various modified AuNPs. The surface of AuNPs and Au electrode was coated with polymer films, as determined by Fourier transform infrared spectroscopy and atomic force microscopy. Measurements obtained for various AuNPs and the plasma-treated surface of the Au electrode were compared with those obtained for an untreated Au electrode. According to the resonant frequency shift of QCM, a linear relationship was observed that significantly differed for AuNPs, MUA-AuNPs, and DCT-AuNPs (R 2 range, 0.94–0.965, 0.934–0.972, and 0.874–0.9514, respectively). Compared to inductively coupled plasma and micro-computerized tomography, the QCM method with plasma treatment has advantages of real-time monitoring, greater sensitivity, and lower cost. Our results demonstrate that surface modifications measured by a QCM system for various modified AuNPs were reliable.

  6. Preparation of a molecularly imprinted sensor based on quartz crystal microbalance for specific recognition of sialic acid in human urine.

    Science.gov (United States)

    Qiu, Xiuzhen; Xu, Xian-Yan; Chen, Xuncai; Wu, Yiyong; Guo, Huishi

    2018-05-08

    A novel molecularly imprinted quartz crystal microbalance (QCM) sensor was successfully prepared for selective determination of sialic acid (SA) in human urine samples. To obtain the QCM sensor, we first modified the gold surface of the QCM chip by self-assembling of allylmercaptane to introduce polymerizable double bonds on the chip surface. Then, SA molecularly imprinted polymer (MIP) nanofilm was attached to the modified QCM chip surface. For comparison, we have also characterized the nonmodified and improved surfaces of the QCM sensor by using atomic force microscopy (AFM) and Fourier transform infrared (FTIR) spectroscopy. We then tested the selectivity and detection limit of the imprinted QCM sensor via a series of adsorption experiments. The results show a linear response in the range of 0.025-0.50 μmol L -1 for sialic acid. Moreover, the limit of detection (LOD) of the prepared imprinted QCM sensor was found to be 1.0 nmol L -1 for sialic acid, and high recovery values range from 87.6 to 108.5% with RSD sensor was developed and used to detect sialic acid in human urine samples. Graphical abstract Specific recognition of sialic acid by the MIP-QCM sensor system.

  7. Real-time monitoring of peptic and tryptic digestions of bovine β-casein using quartz crystal microbalance

    International Nuclear Information System (INIS)

    Huenerbein, Andreas; Schmelzer, Christian E.H.; Neubert, Reinhard H.H.

    2007-01-01

    In this study peptic and tryptic digestions of bovine β-casein were investigated using quartz crystal microbalance (QCM). β-Casein, which was used as a model protein, was immobilized on the surface of the QCM sensor where its degradation caused shifts in the resonant frequency. Atomic force microscopy was applied for the characterization of the protein layer. Different pH-values for peptic or tryptic digestions were chosen to visualize their effect on enzyme activity. Lower frequency shifts were observed at pH-values deviating from those at the maximum enzyme activity. In the case of the peptic digestion the frequency shift at pH 4 was more than 10 times smaller than those at pH 2. The frequency shifts for tryptic digestions at pH 5.4 and pH 6.4 were about two thirds compared to that obtained for the digestion at pH 7.4. The identification of peptides using MALDI-ToF mass spectrometry was used for verification of the proteolyses of the immobilized protein. Furthermore, it was shown that the QCM technique allows close observation of the effect of different pH-values on the immobilized casein layer. All in all, QCM facilitates the monitoring of the progress of enzymatic reactions in real-time

  8. Real-time monitoring of peptic and tryptic digestions of bovine {beta}-casein using quartz crystal microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Huenerbein, Andreas [Institute of Pharmaceutics and Biopharmaceutics, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale) (Germany)]. E-mail: andreas.huenerbein@pharmazie.uni-halle.de; Schmelzer, Christian E.H. [Institute of Pharmaceutics and Biopharmaceutics, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale) (Germany); Neubert, Reinhard H.H. [Institute of Pharmaceutics and Biopharmaceutics, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale) (Germany)

    2007-02-12

    In this study peptic and tryptic digestions of bovine {beta}-casein were investigated using quartz crystal microbalance (QCM). {beta}-Casein, which was used as a model protein, was immobilized on the surface of the QCM sensor where its degradation caused shifts in the resonant frequency. Atomic force microscopy was applied for the characterization of the protein layer. Different pH-values for peptic or tryptic digestions were chosen to visualize their effect on enzyme activity. Lower frequency shifts were observed at pH-values deviating from those at the maximum enzyme activity. In the case of the peptic digestion the frequency shift at pH 4 was more than 10 times smaller than those at pH 2. The frequency shifts for tryptic digestions at pH 5.4 and pH 6.4 were about two thirds compared to that obtained for the digestion at pH 7.4. The identification of peptides using MALDI-ToF mass spectrometry was used for verification of the proteolyses of the immobilized protein. Furthermore, it was shown that the QCM technique allows close observation of the effect of different pH-values on the immobilized casein layer. All in all, QCM facilitates the monitoring of the progress of enzymatic reactions in real-time.

  9. In situ measurement of the mass concentration of flame-synthesized nanoparticles using quartz-crystal microbalance

    International Nuclear Information System (INIS)

    Hevroni, A; Golan, H; Fialkov, A; Tsionsky, V; Markovich, G; Cheskis, S; Rahinov, I

    2011-01-01

    A novel in situ method for measurement of mass concentration of nanoparticles (NPs) formed in flames is proposed. In this method, the deposition rate of NPs collected by a molecular beam sampling system is measured by quartz-crystal microbalance (QCM). It is the only existing method which allows direct measurement of NP mass concentration profiles in flames. The feasibility of the method was demonstrated by studying iron oxide NP formation in low-pressure methane/oxygen/nitrogen flames doped with iron pentacarbonyl. The system was tested under fuel-lean and fuel-rich flame conditions. Good agreement between measured QCM deposition rates and their estimations obtained by the transmission electron microscopy analysis of samples collected from the molecular beam has been demonstrated. The sensitivity of the method is comparable to that of particle mass spectrometry (PMS). Combination of the QCM technique with PMS and/or optical measurements can provide new qualitative information which is important for elucidation of the mechanisms governing the NP flame synthesis

  10. Adsorption Analysis of Lactoferrin to Titanium, Stainless Steel, Zirconia, and Polymethyl Methacrylate Using the Quartz Crystal Microbalance Method

    Directory of Open Access Journals (Sweden)

    Eiji Yoshida

    2016-01-01

    Full Text Available It is postulated that biofilm formation in the oral cavity causes some oral diseases. Lactoferrin is an antibacterial protein in saliva and an important defense factor against biofilm development. We analyzed the adsorbed amount of lactoferrin and the dissociation constant (Kd of lactoferrin to the surface of different dental materials using an equilibrium analysis technique in a 27 MHz quartz crystal microbalance (QCM measurement. Four different materials, titanium (Ti, stainless steel (SUS, zirconia (ZrO2 and polymethyl methacrylate (PMMA, were evaluated. These materials were coated onto QCM sensors and the surfaces characterized by atomic force microscopic observation, measurements of surface roughness, contact angles of water, and zeta potential. QCM measurements revealed that Ti and SUS showed a greater amount of lactoferrin adsorption than ZrO2 and PMMA. Surface roughness and zeta potential influenced the lactoferrin adsorption. On the contrary, the Kd value analysis indicated that the adsorbed lactoferrin bound less tightly to the Ti and SUS surfaces than to the ZrO2 and PMMA surfaces. The hydrophobic interaction between lactoferrin and ZrO2 and PMMA is presumed to participate in better binding of lactoferrin to ZrO2 and PMMA surfaces. It was revealed that lactoferrin adsorption behavior was influenced by the characteristics of the material surface.

  11. Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring.

    KAUST Repository

    Rydberg, Hanna A

    2014-04-18

    Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions.

  12. Humidity scanning quartz crystal microbalance with dissipation monitoring setup for determination of sorption-desorption isotherms and rheological changes

    Energy Technology Data Exchange (ETDEWEB)

    Björklund, Sebastian, E-mail: sebastianbjorklund@gmail.com; Kocherbitov, Vitaly [Department of Biomedical Science, Faculty of Health and Society, Malmö University, Malmö (Sweden); Biofilms—Research Center for Biointerfaces, Malmö University, Malmö (Sweden)

    2015-05-15

    A new method to determine water sorption-desorption isotherms with high resolution in the complete range of water activities (relative humidities) is presented. The method is based on quartz crystal microbalance with dissipation monitoring (QCM-D). The QCM-D is equipped with a humidity module in which the sample film is kept in air with controlled humidity. The experimental setup allows for continuous scanning of the relative humidity from either dry to humid conditions or vice versa. The amount of water sorbed or desorbed from the sample is determined from the resonance frequencies of the coated quartz sensor, via analysis of the overtone dependence. In addition, the method allows for characterization of hydration induced changes of the rheological properties from the dissipation data, which is closely connected to the viscoelasticity of the film. The accuracy of the humidity scanning setup is confirmed in control experiments. Sorption-desorption isotherms of pig gastric mucin and lysozyme, obtained by the new method, show good agreement with previous results. Finally, we show that the deposition technique used to coat the quartz sensor influences the QCM-D data and how this issue can be used to obtain further information on the effect of hydration. In particular, we demonstrate that spin-coating represents an attractive alternative to obtain sorption-desorption isotherms, while drop-coating provides additional information on changes of the rheological properties during hydration.

  13. Peptide-membrane interactions of arginine-tryptophan peptides probed using quartz crystal microbalance with dissipation monitoring.

    KAUST Repository

    Rydberg, Hanna A; Kunze, Angelika; Carlsson, Nils; Altgä rde, Noomi; Svedhem, Sofia; Nordé n, Bengt

    2014-01-01

    Membrane-active peptides include peptides that can cross cellular membranes and deliver macromolecular cargo as well as peptides that inhibit bacterial growth. Some of these peptides can act as both transporters and antibacterial agents. It is desirable to combine the knowledge from these two different fields of membrane-active peptides into design of new peptides with tailored actions, as transporters of cargo or as antibacterial substances, targeting specific membranes. We have previously shown that the position of the amino acid tryptophan in the peptide sequence of three arginine-tryptophan peptides affects their uptake and intracellular localization in live mammalian cells, as well as their ability to inhibit bacterial growth. Here, we use quartz crystal microbalance with dissipation monitoring to assess the induced changes caused by binding of the three peptides to supported model membranes composed of POPC, POPC/POPG, POPC/POPG/cholesterol or POPC/lactosyl PE. Our results indicate that the tryptophan position in the peptide sequence affects the way these peptides interact with the different model membranes and that the presence of cholesterol in particular seems to affect the membrane interaction of the peptide with an even distribution of tryptophans in the peptide sequence. These results give mechanistic insight into the function of these peptides and may aid in the design of membrane-active peptides with specified cellular targets and actions.

  14. Probing adsorption of polyacrylamide-based polymers on anisotropic Basal planes of kaolinite using quartz crystal microbalance.

    Science.gov (United States)

    Alagha, Lana; Wang, Shengqun; Yan, Lujie; Xu, Zhenghe; Masliyah, Jacob

    2013-03-26

    Quartz crystal microbalance with dissipation (QCM-D) was applied to investigate the adsorption characteristics of polyacrylamide-based polymers (PAMs) on anisotropic basal planes of kaolinite. Kaolinite basal planes were differentiated by depositing kaolinite nanoparticles (KNPs) on silica and alumina sensors in solutions of controlled pH values. Adsorption of an in-house synthesized organic-inorganic Al(OH)3-PAM (Al-PAM) as an example of cationic hybrid PAM and a commercially available partially hydrolyzed polyacrylamide (MF1011) as an example of anionic PAM was studied. Cationic Al-PAM was found to adsorb irreversibly and preferentially on tetrahedral silica basal planes of kaolinite. In contrast, anionic MF1011 adsorbed strongly on aluminum-hydroxy basal planes, while its adsorption on tetrahedral silica basal planes was weak and reversible. Adsorption study revealed that both electrostatic attraction and hydrogen-bonding mechanisms contribute to adsorption of PAMs on kaolinite. The adsorbed Al-PAM layer was able to release trapped water overtime and became more compact, while MF1011 film became more dissipative as backbones stretched out from kaolinite surface with minimal overlapping. Experimental results obtained from this study provide clear insights into the phenomenon that governs flocculation-based solid-liquid separation processes using multicomponent flocculants of anionic and cationic nature.

  15. The use of quartz crystal microbalance with dissipation (QCM-D) for studying nanoparticle-induced platelet aggregation

    Science.gov (United States)

    Santos-Martinez, Maria Jose; Inkielewicz-Stepniak, Iwona; Medina, Carlos; Rahme, Kamil; D’Arcy, Deirdre M; Fox, Daniel; Holmes, Justin D; Zhang, Hongzhou; Radomski, Marek Witold

    2012-01-01

    Interactions between blood platelets and nanoparticles have both pharmacological and toxicological significance and may lead to platelet activation and aggregation. Platelet aggregation is usually studied using light aggregometer that neither mimics the conditions found in human microvasculature nor detects microaggregates. A new method for the measurement of platelet microaggregation under flow conditions using a commercially available quartz crystal microbalance with dissipation (QCM-D) has recently been developed. The aim of the current study was to investigate if QCM-D could be used for the measurement of nanoparticle-platelet interactions. Silica, polystyrene, and gold nanoparticles were tested. The interactions were also studied using light aggregometry and flow cytometry, which measured surface abundance of platelet receptors. Platelet activation was imaged using phase contrast and scanning helium ion microscopy. QCM-D was able to measure nanoparticle-induced platelet microaggregation for all nanoparticles tested at concentrations that were undetectable by light aggregometry and flow cytometry. Microaggregates were measured by changes in frequency and dissipation, and the presence of platelets on the sensor surface was confirmed and imaged by phase contrast and scanning helium ion microscopy. PMID:22275839

  16. Determination of functionalized gold nanoparticles incorporated in hydrophilic and hydrophobic microenvironments by surface modification of quartz crystal microbalance

    Science.gov (United States)

    Wu, Tsui-Hsun; Liao, Shu-Chuan; Chen, Ying-Fang; Huang, Yi-You; Wei, Yi-Syuan; Tu, Shu-Ju; Chen, Ko-Shao

    2013-06-01

    In this study, plasma deposition methods were used to immobilize Au electrode of a quartz crystal microbalance (QCM) to create different microenvironments for mass measurement of various modified Au nanoparticles (AuNPs). AuNPs were modified by 11-mercaptoundecanoic acid (MUA) and 1-decanethiol (DCT) for potential applications to drug release, protective coatings, and immunosensors. We aimed to develop a highly sensitive and reliable method to quantify the mass of various modified AuNPs. The surface of AuNPs and Au electrode was coated with polymer films, as determined by Fourier transform infrared spectroscopy and atomic force microscopy. Measurements obtained for various AuNPs and the plasma-treated surface of the Au electrode were compared with those obtained for an untreated Au electrode. According to the resonant frequency shift of QCM, a linear relationship was observed that significantly differed for AuNPs, MUA-AuNPs, and DCT-AuNPs (R2 range, 0.94-0.965, 0.934-0.972, and 0.874-0.9514, respectively). Compared to inductively coupled plasma and micro-computerized tomography, the QCM method with plasma treatment has advantages of real-time monitoring, greater sensitivity, and lower cost. Our results demonstrate that surface modifications measured by a QCM system for various modified AuNPs were reliable.

  17. Investigation of the interaction between liquid and micro/nanostructured surfaces during condensation with quartz crystal microbalance

    Science.gov (United States)

    Su, Junwei

    Dropwise condensation (DWC) on hydrophobic surfaces is attracting attention for its great potential in many industrial applications, such as steam power plants, water desalination, and de-icing of aerodynamic surfaces, to list a few. The direct dynamic characterization of liquid/solid interaction can significantly accelerate the progress toward a full understanding of the thermal and mass transport mechanisms during DWC processes. The research focuses on the development of a novel acoustic-based technique for analyzing the liquid/solid interactions of different condensations on micro- and nanostructured surfaces including DWC. hi addition. the newly developed technology was demonstrated for quantitatively sensing different wetting states of liquid on rough surfaces. First, different micro/nanostructures were fabricated on the quartz crystal microbalance (QCM), which serves as acoustic sensor. Polymethyl methacrylate (PMMA) micropillars, with varying heights from 6.03 to 25.02 microm, were fabricated on a quartz crystal microbalance (QCM) substrate by thermal nanoimprinting lithography to form pillar-based QCM (QCM-P). For nanostructured QCM. a copper layer was deposited on the QCM surface and then nanostructures of copper oxide (CuO) films were formed via chemical oxidation in an alkaline solution. Then, these surfaces were treated to make them superhydrophilic or superhydrophobic using oxygen plasma treatment or with coating of 1H,1 H,2H,2H-perfluorooctyl-trichlorosilane (PFOTS). Based on the geometry of these micro/nanostructures, the relationship between the frequency responses of QCM and the wetting states of these surfaces was theoretically investigated. Different theoretical models were established to describing the frequency shift of the micro- and nanostructured QCM in different wetting states. For the microstructured surface, the cantilever based model and a two-degree-of-freedom dynamic model were applied to predict the frequency shift of the QCM-P in

  18. Carbon-based micro-ball and micro-crystal deposition using filamentary pulsed atmospheric pressure plasma

    International Nuclear Information System (INIS)

    Pothiraja, Ramasamy; Bibinov, Nikita; Awakowicz, Peter

    2014-01-01

    Thin plasma filaments are produced by the propagation of ionization waves from a spiked driven electrode in a quartz tube in an argon/methane gas mixture (2400 sccm/2 sccm) at atmospheric pressure. The position of the touch point of filaments on the substrate surface is controlled in our experiment by applying various suitable substrate configurations and geometries of the grounded electrode. The gas conditions at the touch point are varied from argon to ambient air. Based on microphotography and discharge current waveforms, the duration of the filament touching the substrate is estimated to be about one microsecond. Carbon-based materials are deposited during this time at the touch points on the substrate surface. Micro-balls are produced if the filament touch points are saved from ambient air by the argon flow. Under an air admixture, micro-crystals are formed. The dimension of both materials is approximately one micrometre (0.5–2 µm) and corresponds to about 10 10 –10 12 carbon atoms. Neither the diffusion of neutral species nor drift of ions can be reason for the formation of such a big micro-material during this short period of filament–substrate interaction. It is possible that charged carbon-based materials are formed in the plasma channel and transported to the surface of the substrate. The mechanism of this transport and characterization of micro-materials, which are formed under different gas conditions in our experiment, will be studied in the future. (paper)

  19. An Electrochemical Quartz Crystal Microbalance Multisensor System Based on Phthalocyanine Nanostructured Films: Discrimination of Musts

    Directory of Open Access Journals (Sweden)

    Celia Garcia-Hernandez

    2015-11-01

    Full Text Available An array of electrochemical quartz crystal electrodes (EQCM modified with nanostructured films based on phthalocyanines was developed and used to discriminate musts prepared from different varieties of grapes. Nanostructured films of iron, nickel and copper phthalocyanines were deposited on Pt/quartz crystals through the Layer by Layer technique by alternating layers of the corresponding phthalocyanine and poly-allylamine hydrochloride. Simultaneous electrochemical and mass measurements were used to study the mass changes accompanying the oxidation of electroactive species present in must samples obtained from six Spanish varieties of grapes (Juan García, Prieto Picudo, Mencía Regadío, Cabernet Sauvignon, Garnacha and Tempranillo. The mass and voltammetric outputs were processed using three-way models. Parallel Factor Analysis (PARAFAC was successfully used to discriminate the must samples according to their variety. Multi-way partial least squares (N-PLS evidenced the correlations existing between the voltammetric data and the polyphenolic content measured by chemical methods. Similarly, N-PLS showed a correlation between mass outputs and parameters related to the sugar content. These results demonstrated that electronic tongues based on arrays of EQCM sensors can offer advantages over arrays of mass or voltammetric sensors used separately.

  20. Single-pulse and burst-mode ablation of gold films measured by quartz crystal microbalance

    Science.gov (United States)

    Andrusyak, Oleksiy G.; Bubelnik, Matthew; Mares, Jeremy; McGovern, Theresa; Siders, Craig W.

    2005-02-01

    Femtosecond ablation has several distinct advantages: the threshold energy fluence for the onset of damage and ablation is orders of magnitude less than for traditional nanosecond laser machining, and by virtue of the rapid material removal of approximately an optical penetration depth per pulse, femtosecond machined cuts can be cleaner and more precise than those made with traditional nanosecond or longer pulse lasers. However, in many materials of interest, especially metals, this limits ablation rates to 10-100 nm/pulse. We present the results of using multiple pulse bursts to significantly increase the per-burst ablation rate compared to a single pulse with the same integrated energy, while keeping the peak intensity of each individual pulse below the air ionization limit. Femtosecond ablation with pulses centered at 800-nm having integrated energy of up to 30 mJ per pulse incident upon thin gold films was measured via resonance frequency shifts in a gold-electrode-coated quartz-crystal oscillator. Measurements were performed using Michelson-interferometer-based burst generators, with up to 2 ns pulse separations, as well as pulse shaping by programmable acousto-optic dispersive filter (Dazzler from FastLite) with up to 2 ps pulse separations.

  1. 3D DNA Origami Crystals.

    Science.gov (United States)

    Zhang, Tao; Hartl, Caroline; Frank, Kilian; Heuer-Jungemann, Amelie; Fischer, Stefan; Nickels, Philipp C; Nickel, Bert; Liedl, Tim

    2018-05-18

    3D crystals assembled entirely from DNA provide a route to design materials on a molecular level and to arrange guest particles in predefined lattices. This requires design schemes that provide high rigidity and sufficiently large open guest space. A DNA-origami-based "tensegrity triangle" structure that assembles into a 3D rhombohedral crystalline lattice with an open structure in which 90% of the volume is empty space is presented here. Site-specific placement of gold nanoparticles within the lattice demonstrates that these crystals are spacious enough to efficiently host 20 nm particles in a cavity size of 1.83 × 10 5 nm 3 , which would also suffice to accommodate ribosome-sized macromolecules. The accurate assembly of the DNA origami lattice itself, as well as the precise incorporation of gold particles, is validated by electron microscopy and small-angle X-ray scattering experiments. The results show that it is possible to create DNA building blocks that assemble into lattices with customized geometry. Site-specific hosting of nano objects in the optically transparent DNA lattice sets the stage for metamaterial and structural biology applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. 3D DNA Crystals and Nanotechnology

    Directory of Open Access Journals (Sweden)

    Paul J. Paukstelis

    2016-08-01

    Full Text Available DNA’s molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

  3. Measurement of deposition rate and ion energy distribution in a pulsed dc magnetron sputtering system using a retarding field analyzer with embedded quartz crystal microbalance.

    Science.gov (United States)

    Sharma, Shailesh; Gahan, David; Scullin, Paul; Doyle, James; Lennon, Jj; Vijayaraghavan, Rajani K; Daniels, Stephen; Hopkins, M B

    2016-04-01

    A compact retarding field analyzer with embedded quartz crystal microbalance has been developed to measure deposition rate, ionized flux fraction, and ion energy distribution arriving at the substrate location. The sensor can be placed on grounded, electrically floating, or radio frequency (rf) biased electrodes. A calibration method is presented to compensate for temperature effects in the quartz crystal. The metal deposition rate, metal ionization fraction, and energy distribution of the ions arriving at the substrate location are investigated in an asymmetric bipolar pulsed dc magnetron sputtering reactor under grounded, floating, and rf biased conditions. The diagnostic presented in this research work does not suffer from complications caused by water cooling arrangements to maintain constant temperature and is an attractive technique for characterizing a thin film deposition system.

  4. Measurement of deposition rate and ion energy distribution in a pulsed dc magnetron sputtering system using a retarding field analyzer with embedded quartz crystal microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Shailesh, E-mail: shailesh.sharma6@mail.dcu.ie [Dublin City University, Glasnevin, Dublin 9 (Ireland); Impedans Limited, Chase House, City Junction Business Park, Northern Cross, D17 AK63, Dublin 17 (Ireland); Gahan, David, E-mail: david.gahan@impedans.com; Scullin, Paul; Doyle, James; Lennon, Jj; Hopkins, M. B. [Impedans Limited, Chase House, City Junction Business Park, Northern Cross, D17 AK63, Dublin 17 (Ireland); Vijayaraghavan, Rajani K.; Daniels, Stephen [Dublin City University, Glasnevin, Dublin 9 (Ireland)

    2016-04-15

    A compact retarding field analyzer with embedded quartz crystal microbalance has been developed to measure deposition rate, ionized flux fraction, and ion energy distribution arriving at the substrate location. The sensor can be placed on grounded, electrically floating, or radio frequency (rf) biased electrodes. A calibration method is presented to compensate for temperature effects in the quartz crystal. The metal deposition rate, metal ionization fraction, and energy distribution of the ions arriving at the substrate location are investigated in an asymmetric bipolar pulsed dc magnetron sputtering reactor under grounded, floating, and rf biased conditions. The diagnostic presented in this research work does not suffer from complications caused by water cooling arrangements to maintain constant temperature and is an attractive technique for characterizing a thin film deposition system.

  5. Simultaneous detection of surface coverage and structure of krypton films on gold by helium atom diffraction and quartz crystal microbalance techniques.

    Science.gov (United States)

    Danışman, M Fatih; Özkan, Berrin

    2011-11-01

    We describe a quartz crystal microbalance setup that can be operated at low temperatures in ultra high vacuum with gold electrode surfaces acting as substrate surface for helium diffraction measurements. By simultaneous measurement of helium specular reflection intensity from the electrode surface and resonance frequency shift of the crystal during film adsorption, helium diffraction data can be correlated to film thickness. In addition, effects of interfacial viscosity on the helium diffraction pattern could be observed. To this end, first, flat gold films on AT cut quartz crystals were prepared which yield high enough helium specular reflection intensity. Then the crystals were mounted in the helium diffractometer sample holder and driven by means of a frequency modulation driving setup. Different crystal geometries were tested to obtain the best quality factor and preliminary measurements were performed on Kr films on gold surfaces. While the crystal structure and coverage of krypton films as a function of substrate temperature could successfully be determined, no depinning effects could be observed. © 2011 American Institute of Physics

  6. 1-Butyl-3-Methylimidazolium Tetrafluoroborate Film as a Highly Selective Sensing Material for Non-Invasive Detection of Acetone Using a Quartz Crystal Microbalance.

    Science.gov (United States)

    Tao, Wenyan; Lin, Peng; Liu, Sili; Xie, Qingji; Ke, Shanming; Zeng, Xierong

    2017-01-20

    Breath acetone serves as a biomarker for diabetes. This article reports 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF₄]), a type of room temperature ionic liquid (RTIL), as a selective sensing material for acetone. The RTIL sensing layer was coated on a quartz crystal microbalance (QCM) for detection. The sensing mechanism is based on a decrease in viscosity and density of the [bmim][BF₄] film due to the solubilization of acetone leading to a positive frequency shift in the QCM. Acetone was detected with a linear range from 7.05 to 750 ppmv. Sensitivity and limit of detection were found to be 3.49 Hz/ppmv and 5.0 ppmv, respectively. The [bmim][BF₄]-modified QCM sensor demonstrated anti-interference ability to commonly found volatile organic compounds in breath, e.g., isoprene, 1,2-pentadiene, d -limonene, and dl -limonene. This technology is useful for applications in non-invasive early diabetic diagnosis.

  7. Immersion angle dependence of the resonant-frequency shift of the quartz crystal microbalance in a liquid: effects of longitudinal wave.

    Science.gov (United States)

    Yoshimoto, Minoru; Kobirata, Satoshi; Aizawa, Hideo; Kurosawa, Shigeru

    2007-06-19

    We investigated the effects of the longitudinal wave on the immersion angle dependence of the resonant-frequency shift, deltaF, of the quartz crystal microbalance, QCM. In order to study exactly the effects, we employed the three types of cells: normal cell, cell with the glass beads and cell with sponge. The longitudinal wave exists in the normal cell. On the other hand, both the cell with the glass beads and the cell with sponge eliminate the longitudinal wave. As results, we have found that the tendencies of deltaF are the same in the three types of cells. That is, we conclude that the longitudinal wave does not have effects on the immersion angle dependence of deltaF.

  8. A survey of the 2001 to 2005 quartz crystal microbalance biosensor literature: applications of acoustic physics to the analysis of biomolecular interactions.

    Science.gov (United States)

    Cooper, Matthew A; Singleton, Victoria T

    2007-01-01

    The widespread exploitation of biosensors in the analysis of molecular recognition has its origins in the mid-1990s following the release of commercial systems based on surface plasmon resonance (SPR). More recently, platforms based on piezoelectric acoustic sensors (principally 'bulk acoustic wave' (BAW), 'thickness shear mode' (TSM) sensors or 'quartz crystal microbalances' (QCM)), have been released that are driving the publication of a large number of papers analysing binding specificities, affinities, kinetics and conformational changes associated with a molecular recognition event. This article highlights salient theoretical and practical aspects of the technologies that underpin acoustic analysis, then reviews exemplary papers in key application areas involving small molecular weight ligands, carbohydrates, proteins, nucleic acids, viruses, bacteria, cells and lipidic and polymeric interfaces. Key differentiators between optical and acoustic sensing modalities are also reviewed. Copyright (c) 2007 John Wiley & Sons, Ltd.

  9. Crystallization of DNA-coated colloids

    Science.gov (United States)

    Wang, Yu; Wang, Yufeng; Zheng, Xiaolong; Ducrot, Étienne; Yodh, Jeremy S.; Weck, Marcus; Pine, David J.

    2015-01-01

    DNA-coated colloids hold great promise for self-assembly of programmed heterogeneous microstructures, provided they not only bind when cooled below their melting temperature, but also rearrange so that aggregated particles can anneal into the structure that minimizes the free energy. Unfortunately, DNA-coated colloids generally collide and stick forming kinetically arrested random aggregates when the thickness of the DNA coating is much smaller than the particles. Here we report DNA-coated colloids that can rearrange and anneal, thus enabling the growth of large colloidal crystals from a wide range of micrometre-sized DNA-coated colloids for the first time. The kinetics of aggregation, crystallization and defect formation are followed in real time. The crystallization rate exhibits the familiar maximum for intermediate temperature quenches observed in metallic alloys, but over a temperature range smaller by two orders of magnitude, owing to the highly temperature-sensitive diffusion between aggregated DNA-coated colloids. PMID:26078020

  10. Bacterial interactions with proteins and cells relevant to the development of life-threatening endocarditis studied by use of a quartz-crystal microbalance.

    Science.gov (United States)

    Krajewski, Stefanie; Rheinlaender, Johannes; Ries, Philip; Canjuga, Denis; Mack, Carmen; Scheideler, Lutz; Schäffer, Tilman E; Geis-Gerstorfer, Jürgen; Wendel, Hans-Peter; Rupp, Frank

    2014-05-01

    Implant-related infections are a major challenge in clinical routine because of severe complications, for example infective endocarditis (IE). The purpose of this study was to investigate the real-time interaction of S. gordonii with proteins and cells important in the development of IE, in a flow system, by use of a quartz-crystal microbalance (QCM). Acoustic sensors were biologically modified by preconditioning with sterile saliva, platelet-poor plasma (PPP), or platelet-rich plasma (PRP), followed then by perfusion of a bacterial suspension. After perfusion, additional fluorescence and scanning electron microscopic (SEM) studies were performed. The surface structure of S. gordonii was analyzed by atomic force microscopy (AFM). Compared with S. gordonii adhesion on the abiotic sensor surface following normal mass loading indicated by a frequency decrease, adhesion on saliva, PPP, or PRP-conditioned sensors resulted in an increase in frequency. Furthermore, adhesion induced slightly increased damping signals for saliva and PPP-coated sensors but a decrease upon bacterial adhesion to PRP, indicating the formation of a more rigid biofilm. Microscopic analysis confirmed the formation of dense and vital bacterial layers and the aggregation of platelets and bacteria. In conclusion, our study shows that the complex patterns of QCM output data observed are strongly dependent on the biological substrate and adhesion mechanisms of S. gordonii. Overall, QCM sheds new light on the pathways of such severe infections as IE.

  11. Interaction analysis of chimeric metal-binding green fluorescent protein and artificial solid-supported lipid membrane by quartz crystal microbalance and atomic force microscopy

    International Nuclear Information System (INIS)

    Prachayasittikul, Virapong; Na Ayudhya, Chartchalerm Isarankura; Hilterhaus, Lutz; Hinz, Andreas; Tantimongcolwat, Tanawut; Galla, Hans-Joachim

    2005-01-01

    Non-specific adsorption and specific interaction between a chimeric green fluorescent protein (GFP) carrying metal-binding region and the immobilized zinc ions on artificial solid-supported lipid membranes was investigated using the quartz crystal microbalance technique and the atomic force microscopy (AFM). Supported lipid bilayer, composed of octanethiol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dioleoyl-sn-glycero-3-[N- (5-amino-1-carboxypentyl iminodiacetic acid)succinyl] (NTA-DOGS)-Zn 2+ , was formed on the gold electrode of quartz resonator (5 MHz). Binding of the chimeric GFP to zinc ions resulted in a rapid decrease of resonance frequency. Reversibility of the process was demonstrated via the removal of metal ions by EDTA. Nanoscale structural orientation of the chimeric GFP on the membrane was imaged by AFM. Association constant of the specific binding to metal ions was 2- to 3-fold higher than that of the non-specific adsorption, which was caused by the fluidization effect of the metal-chelating lipid molecules as well as the steric hindrance effect. This infers a possibility for a further development of biofunctionalized membrane. However, maximization is needed in order to attain closer advancement to a membrane-based sensor device

  12. Trend of telomerase activity change during human iPSC self-renewal and differentiation revealed by a quartz crystal microbalance based assay

    Science.gov (United States)

    Zhou, Yitian; Zhou, Ping; Xin, Yinqiang; Wang, Jie; Zhu, Zhiqiang; Hu, Ji; Wei, Shicheng; Ma, Hongwei

    2014-11-01

    Telomerase plays an important role in governing the life span of cells for its capacity to extend telomeres. As high activity of telomerase has been found in stem cells and cancer cells specifically, various methods have been developed for the evaluation of telomerase activity. To overcome the time-consuming procedures and complicated manipulations of existing methods, we developed a novel method named Telomeric Repeat Elongation Assay based on Quartz crystal microbalance (TREAQ) to monitor telomerase activity during the self-renewal and differentiation of human induced pluripotent stem cells (hiPSCs). TREAQ results indicated hiPSCs possess invariable telomerase activity for 11 passages on Matrigel and a steady decline of telomerase activity when differentiated for different periods, which is confirmed with existing golden standard method. The pluripotency of hiPSCs during differentiation could be estimated through monitoring telomerase activity and compared with the expression levels of markers of pluripotency gene via quantitative real time PCR. Regular assessment for factors associated with pluripotency or stemness was expensive and requires excessive sample consuming, thus TREAQ could be a promising alternative technology for routine monitoring of telomerase activity and estimate the pluripotency of stem cells.

  13. Results from a Novel Method for Corrosion Studies of Electroplated Lithium Metal Based on Measurements with an Impedance Scanning Electrochemical Quartz Crystal Microbalance

    Directory of Open Access Journals (Sweden)

    Martin Winter

    2013-07-01

    Full Text Available A new approach to study the chemical stability of electrodeposited lithium on a copper metal substrate via measurements with a fast impedance scanning electrochemical quartz crystal microbalance is presented. The corrosion of electrochemically deposited lithium was compared in two different electrolytes, based on lithium difluoro(oxalato borate (LiDFOB and lithium hexafluorophosphate, both salts being dissolved in solvent blends of ethylene carbonate and diethyl carbonate. For a better understanding of the corrosion mechanisms, scanning electron microscopy images of electrodeposited lithium were also consulted. The results of the EQCM experiments were supported by AC impedance measurements and clearly showed two different corrosion mechanisms caused by the different salts and the formed SEIs. The observed mass decrease of the quartz sensor of the LiDFOB-based electrolyte is not smooth, but rather composed of a series of abrupt mass fluctuations in contrast to that of the lithium hexafluorophosphate-based electrolyte. After each slow decrease of mass a rather fast increase of mass is observed several times. The slow mass decrease can be attributed to a consolidation process of the SEI or to the partial dissolution of the SEI leaving finally lithium metal unprotected so that a fast film formation sets in entailing the observed fast mass increases.

  14. 1-Butyl-3-Methylimidazolium Tetrafluoroborate Film as a Highly Selective Sensing Material for Non-Invasive Detection of Acetone Using a Quartz Crystal Microbalance

    Directory of Open Access Journals (Sweden)

    Wenyan Tao

    2017-01-01

    Full Text Available Breath acetone serves as a biomarker for diabetes. This article reports 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4], a type of room temperature ionic liquid (RTIL, as a selective sensing material for acetone. The RTIL sensing layer was coated on a quartz crystal microbalance (QCM for detection. The sensing mechanism is based on a decrease in viscosity and density of the [bmim][BF4] film due to the solubilization of acetone leading to a positive frequency shift in the QCM. Acetone was detected with a linear range from 7.05 to 750 ppmv. Sensitivity and limit of detection were found to be 3.49 Hz/ppmv and 5.0 ppmv, respectively. The [bmim][BF4]-modified QCM sensor demonstrated anti-interference ability to commonly found volatile organic compounds in breath, e.g., isoprene, 1,2-pentadiene, d-limonene, and dl-limonene. This technology is useful for applications in non-invasive early diabetic diagnosis.

  15. Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction.

    Science.gov (United States)

    Wang, Dingzhong; Tang, Wei; Wu, Xiaojie; Wang, Xinyi; Chen, Gengjia; Chen, Qiang; Li, Na; Liu, Feng

    2012-08-21

    Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.

  16. Separate measurement of the density and viscosity of a liquid using a quartz crystal microbalance based on admittance analysis (QCM-A)

    International Nuclear Information System (INIS)

    Itoh, Atsushi; Ichihashi, Motoko

    2011-01-01

    We previously used a quartz crystal microbalance (QCM) to identify a frequency f 2 that allows measurement of the mass load without being affected by the viscous load of a liquid in the liquid phase. Here, we determined that frequency in order to separately measure the density and viscosity of a Newtonian liquid. Martin et al separately measured the density and viscosity of a liquid by immersing two quartz resonators, i.e. a smooth-surface resonator and a textured-surface resonator, in the liquid. We used a QCM based on admittance analysis (QCM-A) in the current study to separately measure the viscosity and density of a liquid using only a textured-surface resonator. In the current experiments, we measured the density and viscosity of 500 µl of 10%, 30%, and 50% aqueous glycerol solutions and compared the measured values to reference values. The density obtained had an error of ±1.5% of reference values and the viscosity had an error of about ±5% of reference values. Similar results were obtained with 500 µl of 10%, 30%, and 50% ethanol solutions. Measurement was possible with a quartz resonator, so measurements were made with even smaller samples. The density and viscosity of a liquid were successfully determined with an extremely small amount of liquid, i.e. 10 µl, with almost the same precision as when using 500 µl of the liquid

  17. Particle Characterization for a Protein Drug Product Stored in Pre-Filled Syringes Using Micro-Flow Imaging, Archimedes, and Quartz Crystal Microbalance with Dissipation.

    Science.gov (United States)

    Zheng, Songyan; Puri, Aastha; Li, Jinjiang; Jaiswal, Archana; Adams, Monica

    2017-01-01

    Micro-flow imaging (MFI) has been used for formulation development for analyzing sub-visible particles. Archimedes, a novel technique for analyzing sub-micron particles, has been considered as an orthogonal method to currently existing techniques. This study utilized these two techniques to investigate the effectiveness of polysorbate (PS-80) in mitigating the particle formation of a therapeutic protein formulation stored in silicone oil-coated pre-filled syringes. The results indicated that PS-80 prevented the formation of both protein and silicone oil particles. In the case of protein particles, PS-80 might involve in the interactions with the hydrophobic patches of protein, air bubbles, and the stressed surfaces of silicone oil-coated pre-filled syringes. Such interactions played a role in mitigating the formation of protein particles. Subsequently, quartz crystal microbalance with dissipation (QCM-D) was utilized to characterize the interactions associated with silicone oil, protein, and PS-80 in the solutions. Based on QCM-D results, we proposed that PS-80 likely formed a layer on the interior surfaces of syringes. As a result, the adsorbed PS-80 might block the leakage of silicone oil from the surfaces to solution so that the silicone oil particles were mitigated at the presence of PS-80. Overall, this study demonstrated the necessary of utilizing these three techniques cooperatively in order to better understand the interfacial role of PS-80 in mitigating the formation of protein and silicone oil particles.

  18. Electrochemistry, surface plasmon resonance, and quartz crystal microbalance: an associative study on cytochrome c adsorption on pyridine tail-group monolayers on gold.

    Science.gov (United States)

    Paulo, Tércio de F; de Sousa, Ticyano P; de Abreu, Dieric S; Felício, Nathalie H; Bernhardt, Paul V; Lopes, Luiz G de F; Sousa, Eduardo H S; Diógenes, Izaura C N

    2013-07-25

    Quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and electrochemistry techniques were used to study the electron-transfer (ET) reaction of cytochrome c (Cyt c) on gold surfaces modified with thionicotinamide, thioisonicotinamide, 4-mercaptopyridine, 5-(4-pyridyl)-1,3,4-oxadiazole-2-thiol, 5-phenyl-1,3,4-oxadiazole-2-thiol, 4,4'-bipyridine, and 4,4'-dithiopyridine. The electrochemical results showed that the ET process is complex, being chiefly diffusional with steps depending on the orientation of the pyridine or phenyl tail group of the modifiers. The correlation between the electrochemical results and those acquired by SPR and QCM indicated the presence of an adlayer of Cyt c adsorbed on the thiolate SAMs. This adlayer, although being not electroactive, is essential to assess the ET reaction of Cyt c in solution. The results presented in this work are consistent with the statement (Feng, Z. Q.; Imabayashi, S.; Kakiuchi, T.; Niki, K. J. Electroanal. Chem. 1995, 394, 149-154) that the ET reaction of Cyt c can be explained in terms of the through-bond tunneling mechanism.

  19. Molecularly imprinted polymer based quartz crystal microbalance sensor system for sensitive and label-free detection of synthetic cannabinoids in urine.

    Science.gov (United States)

    Battal, Dilek; Akgönüllü, Semra; Yalcin, M Serkan; Yavuz, Handan; Denizli, Adil

    2018-07-15

    Herein, we prepared a novel quartz crystal microbalance (QCM) sensor for synthetic cannabinoids (JWH-073, JWH-073 butanoic acid, JWH-018 and JWH-018 pentanoic acid,) detection. Firstly, the synthetic cannabinoid (SCs) imprinted (MIP) and non-imprinted (NIP) nanoparticles were synthesized by mini-emulsion polymerization system. The SCs-imprinted nanoparticles were first characterized by SEM, TEM, zeta-size and FTIR-ATR analysis and then were dropped onto the gold QCM surface. The SCs-imprinted QCM sensor was characterized by an ellipsometer, contact angle, and AFM. The limit of detection was found as 0.3, 0.45, 0.4, 0.2 pg/mL JWH-018, JWH-073, JWH-018 pentanoic acid and JWH-073 butanoic acid, respectively. The selectivity of the SCs-imprinted QCM sensor was shown by using JWH-018, JWH-018 pentanoic acid, JWH-073 and JWH-073 butanoic acid. According to the results, the SCs-imprinted QCM sensors show highly selective and sensitive in a broad range of synthetic cannabinoid concentrations (0.0005-1.0 ng/mL) in both aqueous and synthetic urine solutions. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Quartz Crystal Microbalance Coated with Sol-gel-derived Thin Films as Gas Sensor for NO Detection

    Directory of Open Access Journals (Sweden)

    S. J. O’Shea

    2003-10-01

    Full Text Available This paper presents the possibilities and properties of Indium tin oxide (ITO-covered quartz crystal as a NOx toxic gas-sensor. The starting sol-gel solution was prepared by mixing indium chloride dissolved in acetylacetone and tin chloride dissolved in ethanol (0-20% by weight. The ITO thin films were deposited on the gold electrodes of quartz crystal by spin-coating technique and subsequently followed a standard photolithography to pattern the derived films to ensure all sensors with the same sensing areas. All heat treatment processes were controlled below 500°C in order to avoid the piezoelectric characteristics degradation of quartz crystal (Quartz will lose its piezoelectricity at ~573°C due to the phase change from α to β. The electrical and structural properties of ITO thin films were characterized with Hall analysis system, TG/DTA, XRD, XPS, SEM and etc. The gas sensor had featured with ITO thin films of ~100nm as the receptor to sense the toxic gas NO and quartz crystal with frequency of 10MHz as the transducer to transfer the surface reactions (mass loading, etc into the frequency shift. A homemade setup had been employed to measure the sensor response under the static mode. The experimental results had indicated that the ITO-coated QCM had a good sensitivity for NO gas, ~12Hz/100ppm within 5mins. These results prove that the ITO-covered quartz crystals are usable as a gas sensor and as an analytical device.

  1. A quick responding quartz crystal microbalance sensor array based on molecular imprinted polyacrylic acids coating for selective identification of aldehydes in body odor.

    Science.gov (United States)

    Jha, Sunil K; Hayashi, Kenshi

    2015-03-01

    In present work, a novel quartz crystal microbalance (QCM) sensor array has been developed for prompt identification of primary aldehydes in human body odor. Molecularly imprinted polymers (MIP) are prepared using the polyacrylic acid (PAA) polymer matrix and three organic acids (propenoic acid, hexanoic acid and octanoic acid) as template molecules, and utilized as QCM surface coating layer. The performance of MIP films is characterized by 4-element QCM sensor array (three coated with MIP layers and one with pure PAA for reference) dynamic and static responses to target aldehydes: hexanal, heptanal, and nonanal in single, binary, and tertiary mixtures at distinct concentrations. The target aldehydes were selected subsequent to characterization of body odor samples with solid phase-micro extraction gas chromatography mass spectrometer (SPME-GC-MS). The hexanoic acid and octanoic acid imprinted PAA exhibit fast response, and better sensitivity, selectivity and reproducibility than the propenoic acid, and non-imprinted PAA in array. The response time and recovery time for hexanoic acid imprinted PAA are obtained as 5 s and 12 s respectively to typical concentrations of binary and tertiary mixtures of aldehydes using the static response. Dynamic sensor array response matrix has been processed with principal component analysis (PCA) for visual, and support vector machine (SVM) classifier for quantitative identification of target odors. Aldehyde odors were identified successfully in principal component (PC) space. SVM classifier results maximum recognition rate 79% for three classes of binary odors and 83% including single, binary, and tertiary odor classes in 3-fold cross validation. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Transient kinetic studies of pH-dependent hydrolyses by exo-type carboxypeptidase P on a 27-MHz quartz crystal microbalance.

    Science.gov (United States)

    Furusawa, Hiroyuki; Takano, Hiroki; Okahata, Yoshio

    2008-02-15

    pH-Dependent kinetic parameters (k(on), k(off), and k(cat)) of protein (myoglobin) hydrolyses catalyzed by exo-enzyme (carboxypeptidase P, CPP) were obtained by using a protein-immobilized quartz crystal microbalance (QCM) in acidic aqueous solutions. The formation of the enzyme-substrate (ES) complex (k(on)), the decay of the ES complex (k(off)), and the formation of the product (k(cat)) could be analyzed by transient kinetics as mass changes on the QCM plate. The Kd (k(off)/k(on)) value was different from the Michaelis constant Km calculated from (k(off) + k(cat))/k(on) due to k(cat) > k(off). The rate-determining step was the binding step (k(on), and the catalytic rate k(cat) was faster than other k(on) and k(off) values. In the range of pH 2.5-5.0, values of k(on) gradually increased with decreasing pH showing a maximum at pH 3.7, values of k(off) were independent of pH, and k(cat) increased gradually with decreasing pH. As a result, the apparent rate constant (k(cat)/Km) showed a maximum at pH 3.7 and gradually increased with decreasing pH. The optimum pH at 3.7 of k(on) is explained by the optimum binding ability of CPP to the COOH terminus of the substrate with hydrogen bonds. The increase of k(cat) at the lower pH correlated with the decrease of alpha-helix contents of the myoglobin substrate on the QCM.

  3. The impact of water and hydrocarbon concentration on the sensitivity of a polymer-based quartz crystal microbalance sensor for organic compounds

    International Nuclear Information System (INIS)

    Pejcic, Bobby; Crooke, Emma; Doherty, Cara M.; Hill, Anita J.; Myers, Matthew; Qi, Xiubin; Ross, Andrew

    2011-01-01

    Highlights: → The response of a polymer coated QCM sensor is affected by water soaking time. → Polymer-water interfacial processes influence the QCM sensitivity for hydrocarbons. → The QCM sensitivity of high Tg polymer films is affected by plasticization processes. - Abstract: Long-term environmental monitoring of organic compounds in natural waters requires sensors that respond reproducibly and linearly over a wide concentration range, and do not degrade with time. Although polymer coated piezoelectric based sensors have been widely used to detect hydrocarbons in aqueous solution, very little information exists regarding their stability and suitability over extended periods in water. In this investigation, the influence of water aging on the response of various polymer membranes [polybutadiene (PB), polyisobutylene (PIB), polystyrene (PS), polystyrene-co-butadiene (PSB)] was studied using the quartz crystal microbalance (QCM). QCM measurements revealed a modest increase in sensitivity towards toluene for PB and PIB membranes at concentrations above 90 ppm after aging in water for 4 days. In contrast, the sensitivity of PS and PSB coated QCM sensors depended significantly on the toluene concentration and increased considerably at concentrations above 90 ppm after aging in water for 4 days. Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) showed that there is a change in the sorption mechanism at higher toluene levels for PS and PSB. Positron annihilation lifetime spectroscopy (PALS) studies were performed to investigate the free volume properties of all polymers and to monitor any changes in the free volume size and distribution due to water and toluene exposure. The PALS did not detect any considerable variation in the free volume properties of the polymer films as a function of solution composition and soaking time, implying that viscoelastic and/or interfacial processes (i.e. surface area changes) are probably responsible

  4. In Situ Real-Time Mechanical and Morphological Characterization of Electrodes for Electrochemical Energy Storage and Conversion by Electrochemical Quartz Crystal Microbalance with Dissipation Monitoring.

    Science.gov (United States)

    Shpigel, Netanel; Levi, Mikhael D; Sigalov, Sergey; Daikhin, Leonid; Aurbach, Doron

    2018-01-16

    Quartz crystal microbalance with dissipation monitoring (QCM-D) generates surface-acoustic waves in quartz crystal plates that can effectively probe the structure of films, particulate composite electrodes of complex geometry rigidly attached to quartz crystal surface on one side and contacting a gas or liquid phase on the other side. The output QCM-D characteristics consist of the resonance frequency (MHz frequency range) and resonance bandwidth measured with extra-ordinary precision of a few tenths of Hz. Depending on the electrodes stiffness/softness, QCM-D operates either as a gravimetric or complex mechanical probe of their intrinsic structure. For at least 20 years, QCM-D has been successfully used in biochemical and environmental science and technology for its ability to probe the structure of soft solvated interfaces. Practical battery and supercapacitor electrodes appear frequently as porous solids with their stiffness changing due to interactions with electrolyte solutions or as a result of ion intercalation/adsorption and long-term electrode cycling. Unfortunately, most QCM measurements with electrochemical systems are carried out based on a single (fundamental) frequency and, as such, provided that the resonance bandwidth remains constant, are suitable for only gravimetric sensing. The multiharmonic measurements have been carried out mainly on conducting/redox polymer films rather than on typical composite battery/supercapacitor electrodes. Here, we summarize the most recent publications devoted to the development of electrochemical QCM-D (EQCM-D)-based methodology for systematic characterization of mechanical properties of operating battery/supercapacitor electrodes. By varying the electrodes' composition and structure (thin/thick layers, small/large particles, binders with different mechanical properties, etc.), nature of the electrolyte solutions and charging/cycling conditions, the method is shown to be operated in different application modes. A

  5. Combined atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and quartz crystal microbalance (QCM) studies of glucose oxidase (GOx) immobilised onto self-assembled monolayer on the gold film

    International Nuclear Information System (INIS)

    Losic, D.; Shapter, J.; Gooding, J.; Erokin, P.; Short, K.

    1999-01-01

    In fabrication of biosensors, self-assembled monolayers (SAM) are an attractive method of immobilising enzymes at electrode surface since it allows precise control over the amount and spatial distribution of the immobilized enzyme. The covalent attachment of glucose oxidase (GOx) to a carboxylic terminated SAM chemisorbed onto gold films was achieved via carbodiimide activation of the carboxylic acids to a reactive intermediate susceptible to nucleophilic attack by amines on free lysine chains of the enzyme. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS) and quartz crystal microbalance (QCM) measurements were used for characterisation of GOx modified gold surfaces. Tapping mode AFM studies have revealed that GOx molecules form slightly disordered arrays of pentagonal or hexagonal clusters. Observed features of immobilised GOx are distributed as a submonolayer on the SAM surface which has allowed visualisation of native and unfolded enzyme structure. The presence of the SAM and enzyme on the gold surface was detected by XPS spectroscopy. Spectra show typical peaks for the C 1s, O 1s and N 1s regions. A kinetic study of the adsorption of GOx onto activated SAM using in-situ QCM allowed determination the amount of immobilised GOx on the layer and consequently the optimal immobilisation conditions. Performance parameters of the biosensor such as sensitivity to glucose concentration as a function of enzyme loading were evaluated amperometrically using the redox mediator p-benzoquinone

  6. The use of a quartz crystal microbalance as an analytical tool to monitor particle/surface and particle/particle interactions under dry ambient and pressurized conditions: a study using common inhaler components.

    Science.gov (United States)

    Turner, N W; Bloxham, M; Piletsky, S A; Whitcombe, M J; Chianella, I

    2016-12-19

    Metered dose inhalers (MDI) and multidose powder inhalers (MPDI) are commonly used for the treatment of chronic obstructive pulmonary diseases and asthma. Currently, analytical tools to monitor particle/particle and particle/surface interaction within MDI and MPDI at the macro-scale do not exist. A simple tool capable of measuring such interactions would ultimately enable quality control of MDI and MDPI, producing remarkable benefits for the pharmaceutical industry and the users of inhalers. In this paper, we have investigated whether a quartz crystal microbalance (QCM) could become such a tool. A QCM was used to measure particle/particle and particle/surface interactions on the macroscale, by additions of small amounts of MDPI components, in the powder form into a gas stream. The subsequent interactions with materials on the surface of the QCM sensor were analyzed. Following this, the sensor was used to measure fluticasone propionate, a typical MDI active ingredient, in a pressurized gas system to assess its interactions with different surfaces under conditions mimicking the manufacturing process. In both types of experiments the QCM was capable of discriminating interactions of different components and surfaces. The results have demonstrated that the QCM is a suitable platform for monitoring macro-scale interactions and could possibly become a tool for quality control of inhalers.

  7. Preliminary morphological and X-ray diffraction studies of the crystals of the DNA cetyltrimethylammonium salt.

    Science.gov (United States)

    Osica, V D; Pyatigorskaya, T L; Polyvtsev, O F; Dembo, A T; Kliya, M O; Vasilchenko, V N; Verkin, B I; Sukharevskya, B Y

    1977-04-01

    Double-stranded DNA molecules (molecular weight 2.5 X 10(5) - 5 X 10(5) daltons) have been crystallized from water-salt solutions as cetyltrimethylammonium salts (CTA-DNA). Variation of crystallization conditions results in a production of different types of CTA-DNA crystals: spherulits, dendrites, needle-shaped and faceted rhombic crystals, the latter beeing up to 0.3 mm on a side. X-ray diffraction data indicate that DNA molecules in the crystals form a hexagonal lattice which parameters vary slightly with the morphological type of the crystal. Comparison of the melting curves of the DNA preparation before and after crystallization suggests that DNA molecules are partially fractionated in the course of crystallization. Crystals of the CTA-DNA-proflavine complex have also been obtained.

  8. The Role of Repulsion in Colloidal Crystal Engineering with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Soyoung E. [Department; Li, Tao [X-ray; Senesi, Andrew J. [X-ray; Mirkin, Chad A. [Department; Lee, Byeongdu [X-ray

    2017-11-07

    Hybridization interactions between DNA-functionalized nanoparticles (DNA-NPs) can be used to program the crystallization behavior of superlattices, yielding access to complex three-dimensional structures with more than 30 different lattice symmetries. The first superlattice structures using DNA-NPs as building blocks were identified almost two decades ago, yet the role of repulsive interactions in guiding structure formation is still largely unexplored. Here, a com-prehensive approach is taken to study the role of repulsion in the assembly behavior of DNA-NPs, enabling the calculation of interparticle interaction potentials based on experimental results. In this work, we used two different means to assemble DNA-NPs—Watson-Crick base pairing interactions and depletion interactions—and systematically varied the salt concen-tration to study the effective interactions in DNA-NP superlattices. A comparison between the two systems allows us to decouple the repulsive forces from the attractive hybridization interactions that are sensitive to the ionic environment. We find that the gap distance between adjacent DNA-NPs follows a simple power law dependence on solution ionic strength regardless of the type of attractive forces present. This result suggests that the observed trend is driven by repulsive inter-actions. To better understand such behavior, we propose a mean-field model that provides a mathematical description for the observed trend. This model shows that the trend is due to the variation in the effective cross-sectional diameter of DNA duplex and the thickness of DNA shell.

  9. In Situ Adsorption Studies at the Solid/Liquid Interface: Characterization of Biological Surfaces and Interfaces Using Sum Frequency Generation Vibrational Spectroscopy, Atomic Force Microscopy, and Quartz Crystal Microbalance

    International Nuclear Information System (INIS)

    Phillips, D.C.

    2006-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and quartz crystal microbalance (QCM) have been used to study the molecular surface structure, surface topography and mechanical properties, and quantitative adsorbed amount of biological molecules at the solid-liquid interface. The molecular-level behavior of designed peptides adsorbed on hydrophobic polystyrene and hydrophilic silica substrates has been examined as a model of protein adsorption on polymeric biomaterial surfaces. Proteins are such large and complex molecules that it is difficult to identify the features in their structure that lead to adsorption and interaction with solid surfaces. Designed peptides which possess secondary structure provide simple model systems for understanding protein adsorption. Depending on the amino acid sequence of a peptide, different secondary structures (α-helix and β-sheet) can be induced at apolar (air/liquid or air/solid) interfaces. Having a well-defined secondary structure allows experiments to be carried out under controlled conditions, where it is possible to investigate the affects of peptide amino acid sequence and chain length, concentration, buffering effects, etc. on adsorbed peptide structure. The experiments presented in this dissertation demonstrate that SFG vibrational spectroscopy can be used to directly probe the interaction of adsorbing biomolecules with a surface or interface. The use of well designed model systems aided in isolation of the SFG signal of the adsorbing species, and showed that surface functional groups of the substrate are sensitive to surface adsorbates. The complementary techniques of AFM and QCM allowed for deconvolution of the effects of surface topography and coverage from the observed SFG spectra. Initial studies of biologically relevant surfaces are also presented: SFG spectroscopy was used to study the surface composition of common soil bacteria for use in bioremediation of nuclear waste

  10. In Situ Adsorption Studies at the Solid/Liquid Interface:Characterization of Biological Surfaces and Interfaces Using SumFrequency Generation Vibrational Spectroscopy, Atomic Force Microscopy,and Quartz Crystal Microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, Diana Christine [Univ. of California, Berkeley, CA (United States)

    2006-01-01

    Sum frequency generation (SFG) vibrational spectroscopy, atomic force microscopy (AFM), and quartz crystal microbalance (QCM) have been used to study the molecular surface structure, surface topography and mechanical properties, and quantitative adsorbed amount of biological molecules at the solid-liquid interface. The molecular-level behavior of designed peptides adsorbed on hydrophobic polystyrene and hydrophilic silica substrates has been examined as a model of protein adsorption on polymeric biomaterial surfaces. Proteins are such large and complex molecules that it is difficult to identify the features in their structure that lead to adsorption and interaction with solid surfaces. Designed peptides which possess secondary structure provide simple model systems for understanding protein adsorption. Depending on the amino acid sequence of a peptide, different secondary structures (α-helix and β-sheet) can be induced at apolar (air/liquid or air/solid) interfaces. Having a well-defined secondary structure allows experiments to be carried out under controlled conditions, where it is possible to investigate the affects of peptide amino acid sequence and chain length, concentration, buffering effects, etc. on adsorbed peptide structure. The experiments presented in this dissertation demonstrate that SFG vibrational spectroscopy can be used to directly probe the interaction of adsorbing biomolecules with a surface or interface. The use of well designed model systems aided in isolation of the SFG signal of the adsorbing species, and showed that surface functional groups of the substrate are sensitive to surface adsorbates. The complementary techniques of AFM and QCM allowed for deconvolution of the effects of surface topography and coverage from the observed SFG spectra. Initial studies of biologically relevant surfaces are also presented: SFG spectroscopy was used to study the surface composition of common soil bacteria for use in bioremediation of nuclear waste.

  11. Crystallization of DNA fragments from water-salt solutions, containing 2-methylpentane-2,3-diol.

    Science.gov (United States)

    Osica, V D; Sukharevsky, B Y; Vasilchenko, V N; Verkin, B I; Polyvtsev, O F

    1976-09-01

    Fragments of calf thymus DNA have been crystallized by precipitation from water-salt solutions, containing 2-methylpentane-2,3-diol (MPD). DNA crystals usually take the form either of spherulites up to 100 mu in diameter or of needles with the length up to 50 mu. No irreversible denaturation of DNA occurs during the crystallization process. X-ray diffraction from dense slurries of DNA crystals yields crystalline powder patterns.

  12. Anhydrous crystals of DNA bases are wide gap semiconductors.

    Science.gov (United States)

    Maia, F F; Freire, V N; Caetano, E W S; Azevedo, D L; Sales, F A M; Albuquerque, E L

    2011-05-07

    We present the structural, electronic, and optical properties of anhydrous crystals of DNA nucleobases (guanine, adenine, cytosine, and thymine) found after DFT (Density Functional Theory) calculations within the local density approximation, as well as experimental measurements of optical absorption for powders of these crystals. Guanine and cytosine (adenine and thymine) anhydrous crystals are predicted from the DFT simulations to be direct (indirect) band gap semiconductors, with values 2.68 eV and 3.30 eV (2.83 eV and 3.22 eV), respectively, while the experimentally estimated band gaps we have measured are 3.83 eV and 3.84 eV (3.89 eV and 4.07 eV), in the same order. The electronic effective masses we have obtained at band extremes show that, at low temperatures, these crystals behave like wide gap semiconductors for electrons moving along the nucleobases stacking direction, while the hole transport are somewhat limited. Lastly, the calculated electronic dielectric functions of DNA nucleobases crystals in the parallel and perpendicular directions to the stacking planes exhibit a high degree of anisotropy (except cytosine), in agreement with published experimental results.

  13. First results with the Microball and Gammasphere

    International Nuclear Information System (INIS)

    Sarantites, D.G.; Hua, P.F.; LaFosse, D.

    1994-01-01

    The Microball, an improved 4π multi-detector array, was used recently in conjunction with Gammasphere in three experiments. Highlights of the first results are presented here. The Microball consists of 95 CsI(T ell) scintillation detectors with individual Si photodiode readout, arranged in 9 rings. In these first experiments the Microball performed as designed, but the results in new physics exceeded the authors' expectations. They can say with certainty that by its powerful channel selection the Microball enhanced the performance of Gammasphere by one full coincidence fold. This was possible for all exit channels involving charged particle emission, with increasing performance benefit as one progressed to lighter reaction systems. They summarize the essential characteristics of the Microball and give some performance benchmarks. A detailed description of the Microball is given

  14. Molecular engineering of chiral colloidal liquid crystals using DNA origami

    Science.gov (United States)

    Siavashpouri, Mahsa; Wachauf, Christian H.; Zakhary, Mark J.; Praetorius, Florian; Dietz, Hendrik; Dogic, Zvonimir

    2017-08-01

    Establishing precise control over the shape and the interactions of the microscopic building blocks is essential for design of macroscopic soft materials with novel structural, optical and mechanical properties. Here, we demonstrate robust assembly of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular twisted ribbons and two-dimensional colloidal membranes. The exquisite control afforded by the DNA origami technology establishes a quantitative relationship between the microscopic filament structure and the macroscopic cholesteric pitch. Furthermore, it also enables robust assembly of one-dimensional twisted ribbons, which behave as effective supramolecular polymers whose structure and elastic properties can be precisely tuned by controlling the geometry of the elemental building blocks. Our results demonstrate the potential synergy between DNA origami technology and colloidal science, in which the former allows for rapid and robust synthesis of complex particles, and the latter can be used to assemble such particles into bulk materials.

  15. Plasmonic photonic crystals realized through DNA-programmable assembly.

    Science.gov (United States)

    Park, Daniel J; Zhang, Chuan; Ku, Jessie C; Zhou, Yu; Schatz, George C; Mirkin, Chad A

    2015-01-27

    Three-dimensional dielectric photonic crystals have well-established enhanced light-matter interactions via high Q factors. Their plasmonic counterparts based on arrays of nanoparticles, however, have not been experimentally well explored owing to a lack of available synthetic routes for preparing them. However, such structures should facilitate these interactions based on the small mode volumes associated with plasmonic polarization. Herein we report strong light-plasmon interactions within 3D plasmonic photonic crystals that have lattice constants and nanoparticle diameters that can be independently controlled in the deep subwavelength size regime by using a DNA-programmable assembly technique. The strong coupling within such crystals is probed with backscattering spectra, and the mode splitting (0.10 and 0.24 eV) is defined based on dispersion diagrams. Numerical simulations predict that the crystal photonic modes (Fabry-Perot modes) can be enhanced by coating the crystals with a silver layer, achieving moderate Q factors (∼10(2)) over the visible and near-infrared spectrum.

  16. Electrochemical quartz crystal microbalance analysis of the oxygen reduction reaction on Pt-based electrodes. Part 2: adsorption of oxygen species and ClO4(-) anions on Pt and Pt-Co alloy in HClO4 solutions.

    Science.gov (United States)

    Omura, J; Yano, H; Tryk, D A; Watanabe, M; Uchida, H

    2014-01-14

    To gain deeper insight into the role of adsorbed oxygenated species in the O2 reduction reaction (ORR) kinetics on platinum and platinum-cobalt alloys for fuel cells, we carried out a series of measurements with the electrochemical quartz crystal microbalance (EQCM) and the rotating disk electrode (RDE) in acid solution. The effects of anion adsorption on the activities for the ORR were first assessed in HClO4 and HF electrolyte solutions at various concentrations. In our previous work (Part 1), we reported that the perchlorate anion adsorbs specifically on bulk-Pt, with a Frumkin-Temkin isotherm, that is, a linear relationship between Δm and log[HClO4]. Here, we find that the specific adsorption on the Pt-skin/Pt3Co alloy was significantly stronger than that on bulk-Pt, in line with its modified electronic properties. The kinetically controlled current density j(k) for the O2 reduction at the Pt-skin/Pt3Co-RDE was about 9 times larger than that of the bulk-Pt-RDE in 0.01 M HClO4 saturated with air, but the j(k) values on Pt-skin/Pt3Co decreased with increasing [HClO4] more steeply than in the case of Pt, due to the blocking of the active sites by the specifically adsorbed ClO4(-). We have detected reversible mass changes for one or more adsorbed oxygen-containing species (Ox = O2, O, OH, H2O) on the Pt-skin/Pt3Co-EQCM and Pt-EQCM in O2-saturated and He-purged 0.01 M HClO4 solutions, in which the specific adsorption of ClO4(-) anions was negligible. The coverages of oxygen species θ(Ox) on the Pt-skin/Pt3Co in the potential range from 0.86 to 0.96 V in the O2-saturated solution were found to be larger than those on pure Pt, providing strong evidence that the higher O2 reduction activity on the Pt3Co is correlated with higher θ(Ox), contrary to the conventional view.

  17. 40 CFR 86.1312-2007 - Filter stabilization and microbalance workstation environmental conditions, microbalance...

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 19 2010-07-01 2010-07-01 false Filter stabilization and microbalance workstation environmental conditions, microbalance specifications, and particulate matter filter handling and... Particulate Exhaust Test Procedures § 86.1312-2007 Filter stabilization and microbalance workstation...

  18. Thermo-mechanical design and testing of a microbalance for space applications

    Science.gov (United States)

    Scaccabarozzi, Diego; Saggin, Bortolino; Tarabini, Marco; Palomba, Ernesto; Longobardo, Andrea; Zampetti, Emiliano

    2014-12-01

    This work focuses on the thermo-mechanical design of the microbalance used for the VISTA (Volatile In Situ Thermogravimetry Analyzer) sensor. VISTA has been designed to operate in situ in different space environments (asteroids, Mars, icy satellites). In this paper we focus on its application on Mars, where the expected environmental conditions are the most challenging for the thermo-mechanical design. The microbalance holding system has been designed to ensure piezoelectric crystal integrity against the high vibration levels during launch and landing and to cope with the unavoidable thermo-elastic differential displacements due to CTE and temperature differences between the microbalance elements. The crystal holding system, based on three symmetrical titanium supports, provides also the electrical connections needed for crystal actuation, microbalance heating and temperature measurement on the electrode area. On the microbalance crystal surfaces the electrodes, a micro film heater (optimized to perform thermo-gravimetric analysis up to 400 °C) and a resistive thermometer are deposited through a vacuum sputtering process. A mockup of the system has been manufactured and tested at the expected vibration levels and the thermal control effectiveness has been verified in thermo-vacuum environment.

  19. Quartz Crystal Microbalance with Dissipation Monitoring

    Science.gov (United States)

    2014-11-06

    Hydroxyapatite , 10 nm, Sensors • Biotin Functionalized on Gold Sensors • His-tag Capturing Sensor QCM-D techniques provide answers about...mass and structural changes at the nanoscale level. The instrumentation was used to characterize the interaction between small molecules or polymers...The equipment was used mostly for the investigation of interfaces and processes involving silk or silk-based peptides and inorganic components, to

  20. Crystal structure of Mycobacterium tuberculosis O-6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA

    Czech Academy of Sciences Publication Activity Database

    Miggiano, R.; Perugino, G.; Ciaramella, M.; Serpe, M.; Rejman, Dominik; Páv, Ondřej; Pohl, Radek; Garavaglia, S.; Lahiri, S.; Rizzi, M.; Rossi, F.

    2016-01-01

    Roč. 473, č. 2 (2016), s. 123-133 ISSN 0264-6021 EU Projects: European Commission(XE) 241587 - SYSTEMTB Institutional support: RVO:61388963 Keywords : DNA repair * DNA-binding protein * Mycobacterium tuberculosis * O-6-methylguanine-DNA methyltransferase * co-operativity * crystal structure Subject RIV: CE - Biochemistry Impact factor: 3.797, year: 2016

  1. Impact of Heterogeneity and Lattice Bond Strength on DNA Triangle Crystal Growth.

    Science.gov (United States)

    Stahl, Evi; Praetorius, Florian; de Oliveira Mann, Carina C; Hopfner, Karl-Peter; Dietz, Hendrik

    2016-09-07

    One key goal of DNA nanotechnology is the bottom-up construction of macroscopic crystalline materials. Beyond applications in fields such as photonics or plasmonics, DNA-based crystal matrices could possibly facilitate the diffraction-based structural analysis of guest molecules. Seeman and co-workers reported in 2009 the first designed crystal matrices based on a 38 kDa DNA triangle that was composed of seven chains. The crystal lattice was stabilized, unprecedentedly, by Watson-Crick base pairing. However, 3D crystallization of larger designed DNA objects that include more chains such as DNA origami remains an unsolved problem. Larger objects would offer more degrees of freedom and design options with respect to tailoring lattice geometry and for positioning other objects within a crystal lattice. The greater rigidity of multilayer DNA origami could also positively influence the diffractive properties of crystals composed of such particles. Here, we rationally explore the role of heterogeneity and Watson-Crick interaction strengths in crystal growth using 40 variants of the original DNA triangle as model multichain objects. Crystal growth of the triangle was remarkably robust despite massive chemical, geometrical, and thermodynamical sample heterogeneity that we introduced, but the crystal growth sensitively depended on the sequences of base pairs next to the Watson-Crick sticky ends of the triangle. Our results point to weak lattice interactions and high concentrations as decisive factors for achieving productive crystallization, while sample heterogeneity and impurities played a minor role.

  2. Time lapse microscopy of temperature control during self-assembly of 3D DNA crystals

    Science.gov (United States)

    Conn, Fiona W.; Jong, Michael Alexander; Tan, Andre; Tseng, Robert; Park, Eunice; Ohayon, Yoel P.; Sha, Ruojie; Mao, Chengde; Seeman, Nadrian C.

    2017-10-01

    DNA nanostructures are created by exploiting the high fidelity base-pairing interactions of double-stranded branched DNA molecules. These structures present a convenient medium for the self-assembly of macroscopic 3D crystals. In some self-assemblies in this system, crystals can be formed by lowering the temperature, and they can be dissolved by raising it. The ability to monitor the formation and melting of these crystals yields information that can be used to monitor crystal formation and growth. Here, we describe the development of an inexpensive tool that enables direct observation of the crystal growth process as a function of both time and temperature. Using the hanging-drop crystallization of the well-characterized 2-turn DNA tensegrity triangle motif for our model system, its response to temperature has been characterized visually.

  3. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity ...

    Indian Academy of Sciences (India)

    s12039-016-1125-x. Synthesis, X-ray crystal structure, DNA binding and Nuclease activity of lanthanide(III) complexes of 2-benzoylpyridine acetylhydrazone. KARREDDULA RAJA, AKKILI SUSEELAMMA and KATREDDI HUSSAIN REDDY. ∗.

  4. Selective detection of labeled DNA using an air-clad photonic crystal fiber

    DEFF Research Database (Denmark)

    Jensen, Jesper Bo Damm; Hoiby, P.E.; Pedersen, L.H.

    2004-01-01

    Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core.......Demonstration of selective detection of fluorophore labeled DNA by hybridization inside the air holes of a photonic crystal fiber A laser exposes the fiber from the side and the emitted fluorescence tunnels into the core....

  5. Purification, crystallization and preliminary X-ray crystallographic studies of the Mycobacterium tuberculosis DNA gyrase CTD

    International Nuclear Information System (INIS)

    Darmon, Amélie; Piton, Jérémie; Roué, Mélanie; Petrella, Stéphanie; Aubry, Alexandra; Mayer, Claudine

    2012-01-01

    The M. tuberculosis DNA gyrase A C-terminal domain (CTD) was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to space group P2 1 2 1 2 1 and diffraction data were collected to a resolution of 1.55 Å. Mycobacterium tuberculosis DNA gyrase, a nanomachine involved in regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target of fluoroquinolone in the treatment of tuberculosis. The C-terminal domain (CTD) of the DNA gyrase A subunit possesses a unique feature, the ability to wrap DNA in a chiral manner, that plays an essential role during the catalytic cycle. A construct of 36 kDa corresponding to this domain has been overproduced, purified and crystallized. Diffraction data were collected to 1.55 Å resolution. Cleavage of the N-terminal His tag was crucial for obtaining crystals. The crystals belonged to space group P2 1 2 1 2 1 , with one molecule in the asymmetric unit and a low solvent content (33%). This is the first report of the crystallization and preliminary X-ray diffraction studies of a DNA gyrase CTD from a species that contains one unique type II topoisomerase

  6. Following DNA chain extension and protein conformational changes in crystals of a Y-family DNA polymerase via Raman crystallography.

    Science.gov (United States)

    Espinoza-Herrera, Shirly J; Gaur, Vineet; Suo, Zucai; Carey, Paul R

    2013-07-23

    Y-Family DNA polymerases are known to bypass DNA lesions in vitro and in vivo. Sulfolobus solfataricus DNA polymerase (Dpo4) was chosen as a model Y-family enzyme for investigating the mechanism of DNA synthesis in single crystals. Crystals of Dpo4 in complexes with DNA (the binary complex) in the presence or absence of an incoming nucleotide were analyzed by Raman microscopy. (13)C- and (15)N-labeled d*CTP, or unlabeled dCTP, were soaked into the binary crystals with G as the templating base. In the presence of the catalytic metal ions, Mg(2+) and Mn(2+), nucleotide incorporation was detected by the disappearance of the triphosphate band of dCTP and the retention of *C modes in the crystal following soaking out of noncovalently bound C(or *C)TP. The addition of the second coded base, thymine, was observed by adding cognate dTTP to the crystal following a single d*CTP addition. Adding these two bases caused visible damage to the crystal that was possibly caused by protein and/or DNA conformational change within the crystal. When d*CTP is soaked into the Dpo4 crystal in the absence of Mn(2+) or Mg(2+), the primer extension reaction did not occur; instead, a ternary protein·template·d*CTP complex was formed. In the Raman difference spectra of both binary and ternary complexes, in addition to the modes of d(*C)CTP, features caused by ring modes from the template/primer bases being perturbed and from the DNA backbone appear, as well as features from perturbed peptide and amino acid side chain modes. These effects are more pronounced in the ternary complex than in the binary complex. Using standardized Raman intensities followed as a function of time, the C(*C)TP population in the crystal was maximal at ∼20 min. These remained unchanged in the ternary complex but declined in the binary complexes as chain incorporation occurred.

  7. Crystallization and preliminary X-ray crystallographic studies of DnaJ from Streptococcus pneumoniae

    International Nuclear Information System (INIS)

    Zhao, Shasha; Jin, Li; Niu, Siqiang; Yang, Wei; Zhang, Shaocheng; Guo, Zhen; Zhang, Hongpeng; Huang, Ailong; Yin, Yibing; Wang, Deqiang

    2013-01-01

    DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported. DnaJ, cooperating with DnaK and GrpE, promotes the folding of unfolded hydrophobic polypeptides, dissociates protein complexes and translocates protein across membranes. Additionally, DnaJ from Streptococcus pneumoniae (SpDnaJ) is involved in the infectious disease process and is being developed as a potential vaccine to prevent bacterial infection. Here the expression, purification, crystallization and preliminary crystallographic analysis of SpDnaJ are reported. The crystals belong to space groups I222 or I2 1 2 1 2 1 and the diffraction resolution is 3.0 Å with unit-cell parameters a = 47.68, b = 104.45, c = 234.57 Å. The crystal most likely contains one molecule in the asymmetric unit, with a V M value of 3.24 Å 3 Da −1 and a solvent content of 62.1%

  8. Electrochemical characterization of electrolytes and electrodes for lithium-ion batteries. Development of a new measuring method for electrochemical investigations on electrodes with the electrochemical quartz crystal microbalance (EQCM); Elektrochemische Charakterisierung von Elektrolyten und Elektroden fuer Lithium-Ionen-Batterien. Entwicklung einer neuen Messmethode fuer elektrochemische Untersuchungen an Elektroden mit der EQCM

    Energy Technology Data Exchange (ETDEWEB)

    Moosbauer, Dominik Johann

    2010-11-09

    In this work the conductivities of four different lithium salts, LiPF6, LiBF4, LiDFOB, and LiBOB in the solvent mixture EC/DEC (3/7) were investigated. Furthermore, the influence of eight ionic liquids (ILs) as additives on the conductivity and electrochemical stability of lithium salt-based electrolytes was studied. The investigated salts were the well-known lithium LiPF6 and LiDFOB. Conductivity studies were performed over the temperature range (238.15 to 333.15) K. The electrochemical stabilities of the solutions were determined at aluminum electrodes. The salt solubility of LiBF4 and LiDFOB in EC/DEC (3/7) was measured with the quartz crystal microbalance (QCM), a method developed in our group. Moreover, a method to investigate interactions between the electrolyte and electrode components with the electrochemical quartz crystal microbalance (EQCM) was developed. First, investigations of corrosion and passivation effects on aluminum with different lithium salts were performed and masses of deposited products estimated. Therefore, the quartzes were specially prepared with foils. Active materials of cathodes, in this work lithium iron phosphate (LiFePO4), were also investigated with the EQCM by a new method. [German] In dieser Arbeit wurden die Leitfaehigkeiten von vier unterschiedlichen Salzen, LiPF6, LiBF4, LiDFOB und LiBOB in dem Loesemittelgemisch EC/DEC (3/7) untersucht. Des Weiteren wurde der Einfluss von acht Ionischen Fluessigkeiten (ILs) als Additive fuer Lithium-Elektrolyte auf die elektrochemische Stabilitaet und die Leitfaehigkeit studiert. Die untersuchten Salze waren LiPF6 und LiDFOB. Die Leitfaehigkeitsmessungen wurden in einem Temperaturbereich von (238,15 bis 333,15) K durchgefuehrt. Die elektrochemischen Stabilitaeten der Elektrolyte fanden an Aluminium statt. Mit einer an der Arbeitsgruppe entwickelten neuen Methode wurden zudem die Salzloeslichkeiten von LiBF4 und LiDFOB in EC/DEC (3/7) mit der Quarzmikrowaage (QCM) bestimmt. Weiterhin wurden

  9. Controlling the volatility of the written optical state in electrochromic DNA liquid crystals

    Science.gov (United States)

    Liu, Kai; Varghese, Justin; Gerasimov, Jennifer Y.; Polyakov, Alexey O.; Shuai, Min; Su, Juanjuan; Chen, Dong; Zajaczkowski, Wojciech; Marcozzi, Alessio; Pisula, Wojciech; Noheda, Beatriz; Palstra, Thomas T. M.; Clark, Noel A.; Herrmann, Andreas

    2016-05-01

    Liquid crystals are widely used in displays for portable electronic information display. To broaden their scope for other applications like smart windows and tags, new material properties such as polarizer-free operation and tunable memory of a written state become important. Here, we describe an anhydrous nanoDNA-surfactant thermotropic liquid crystal system, which exhibits distinctive electrically controlled optical absorption, and temperature-dependent memory. In the liquid crystal isotropic phase, electric field-induced colouration and bleaching have a switching time of seconds. Upon transition to the smectic liquid crystal phase, optical memory of the written state is observed for many hours without applied voltage. The reorientation of the DNA-surfactant lamellar layers plays an important role in preventing colour decay. Thereby, the volatility of optoelectronic state can be controlled simply by changing the phase of the material. This research may pave the way for developing a new generation of DNA-based, phase-modulated, photoelectronic devices.

  10. Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component.

    Science.gov (United States)

    Hernandez, Carina; Birktoft, Jens J; Ohayon, Yoel P; Chandrasekaran, Arun Richard; Abdallah, Hatem; Sha, Ruojie; Stojanoff, Vivian; Mao, Chengde; Seeman, Nadrian C

    2017-11-16

    There is an increasing appreciation for structural diversity of DNA that is of interest to both DNA nanotechnology and basic biology. Here, we have explored how DNA responds to torsional stress by building on a previously reported two-turn DNA tensegrity triangle and demonstrating that we could introduce an extra nucleotide pair (np) into the original sequence without affecting assembly and crystallization. The extra np imposes a significant torsional stress, which is accommodated by global changes throughout the B-DNA duplex and the DNA lattice. The work reveals a near-atomic structure of naked DNA under a torsional stress of approximately 14%, and thus provides an example of DNA distortions that occur without a requirement for either an external energy source or the free energy available from protein or drug binding. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Crystal structure of the Msx-1 homeodomain/DNA complex.

    Science.gov (United States)

    Hovde, S; Abate-Shen, C; Geiger, J H

    2001-10-09

    The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.

  12. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    Energy Technology Data Exchange (ETDEWEB)

    Barends, Thomas R. M., E-mail: thomas.barends@mpimf-heidelberg.mpg.de [MPI for Medical Research, Heidelberg (Germany); Brosi, Richard W. W. [Freie Universitat Berlin, Berlin (Germany); Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten [MPI for Medical Research, Heidelberg (Germany); Seidel, Ralf [MPI for Molecular Physiology, Dortmund (Germany); Shoeman, Robert L.; Zimmermann, Sabine [MPI for Medical Research, Heidelberg (Germany); Bittl, Robert [Freie Universitat Berlin, Berlin (Germany); Schlichting, Ilme; Reinstein, Jochen [MPI for Medical Research, Heidelberg (Germany)

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

  13. Crystallization of a self-assembled three-dimensional DNA nanostructure

    International Nuclear Information System (INIS)

    Rendek, Kimberly N.; Fromme, Raimund; Grotjohann, Ingo; Fromme, Petra

    2013-01-01

    In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described. The powerful and specific molecular-recognition system present in the base-pairing of DNA allows for the design of a plethora of nanostructures. In this work, the crystallization of a self-assembling three-dimensional B-DNA nanostructure is described. The DNA nanostructure consists of six single-stranded oligonucleotides that hybridize to form a three-dimensional tetrahedron of 80 kDa in molecular mass and 20 bp on each edge. Crystals of the tetrahedron have been successfully produced and characterized. These crystals may form the basis for an X-ray structure of the tetrahedron in the future. Nucleotide crystallography poses many challenges, leading to the fact that only 1352 X-ray structures of nucleic acids have been solved compared with more than 80 000 protein structures. In this work, the crystallization optimization for three-dimensional tetrahedra is also described, with the eventual goal of producing nanocrystals to overcome the radiation-damage obstacle by the use of free-electron laser technology in the future

  14. Solid state radiation chemistry of co-crystallized DNA base pairs studied with EPR and ENDOR

    International Nuclear Information System (INIS)

    Nelson, W.H.; Nimmala, S.; Hole, E.O.; Sagstuen, E.; Close, D.M.

    1995-01-01

    For a number of years, the authors' group has focused on identification of radicals formed from x-irradiation of DNA components by application of EPR and ENDOR spectroscopic techniques to samples in the form of single crystals. With single crystals as samples, it is possible to use the detailed packing and structural information available from x-ray or neutron diffraction reports. This report summarizes results from two crystal systems in which DNA bases are paired by hydrogen bonding. Extensive results are available from one of these, 1-methyl-thymine:9-methyladenine (MTMA), in which the base pairing is the Hoogsteen configuration. Although this configuration is different from that found by Watson-Crick in DNA, nonetheless the hydrogen bond between T(O4) and A(NH 2 ) is present. Although MTMA crystals have been studied previously, the objective was to apply the high-resolution technique of ENDOR to crystals irradiated and studied at temperatures of 10 K or lower in the effort to obtain direct evidence for specific proton transfers. The second system, from which the results are only preliminary, is 9-ethylguanine:1-methyl-5-fluorocytosine (GFC) in which the G:C bases pair is in the Watson Crick configuration. Both crystal systems are anhydrous, so the results include no possible effects from water interactions

  15. Lac repressor: Crystallization of intact tetramer and its complexes with inducer and operator DNA

    International Nuclear Information System (INIS)

    Pace, H.C.; Lu, P.; Lewis, M.

    1990-01-01

    The intact lac repressor tetramer, which regulates expression of the lac operon in Escherichia coli, has been crystallized in the native form, with an inducer, and in a ternary complex with operator DNA and an anti-inducer. The crystals without DNA diffract to better than 3.5 angstrom. They belong to the monoclinic space group C2 and have cell dimensions a = 164.7 angstrom, b = 75.6 angstrom, and c = 161.2 angstrom, with α = γ = 90 degree and β = 125.5 degree. Cocrystals have been obtained with a number of different lac operator-related DNA fragments. The complex with a blunt-ended 16-base-pair strand yielded tetragonal bipyramids that diffract to 6.5 angstrom. These protein-DNA cocrystals crack upon exposure to the gratuitous inducer isopropyl β-D-thiogalactoside, suggesting a conformational change in the repressor-operator complex

  16. Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

    Energy Technology Data Exchange (ETDEWEB)

    Cappadocia, Laurent; Maréchal, Alexandre; Parent, Jean-Sébastien; Lepage, Étienne; Sygusch, Jurgen; Brisson, Normand (Montreal)

    2010-09-07

    DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.

  17. Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA.

    Science.gov (United States)

    Miggiano, Riccardo; Perugino, Giuseppe; Ciaramella, Maria; Serpe, Mario; Rejman, Dominik; Páv, Ondřej; Pohl, Radek; Garavaglia, Silvia; Lahiri, Samarpita; Rizzi, Menico; Rossi, Franca

    2016-01-15

    Mycobacterium tuberculosis O(6)-methylguanine-DNA methyltransferase (MtOGT) contributes to protect the bacterial GC-rich genome against the pro-mutagenic potential of O(6)-methylated guanine in DNA. Several strains of M. tuberculosis found worldwide encode a point-mutated O(6)-methylguanine-DNA methyltransferase (OGT) variant (MtOGT-R37L), which displays an arginine-to-leucine substitution at position 37 of the poorly functionally characterized N-terminal domain of the protein. Although the impact of this mutation on the MtOGT activity has not yet been proved in vivo, we previously demonstrated that a recombinant MtOGT-R37L variant performs a suboptimal alkylated-DNA repair in vitro, suggesting a direct role for the Arg(37)-bearing region in catalysis. The crystal structure of MtOGT complexed with modified DNA solved in the present study reveals details of the protein-protein and protein-DNA interactions occurring during alkylated-DNA binding, and the protein capability also to host unmodified bases inside the active site, in a fully extrahelical conformation. Our data provide the first experimental picture at the atomic level of a possible mode of assembling three adjacent MtOGT monomers on the same monoalkylated dsDNA molecule, and disclose the conformational flexibility of discrete regions of MtOGT, including the Arg(37)-bearing random coil. This peculiar structural plasticity of MtOGT could be instrumental to proper protein clustering at damaged DNA sites, as well as to protein-DNA complexes disassembling on repair. © 2016 Authors; published by Portland Press Limited.

  18. Crystallization and preliminary X-ray characterization of two thermostable DNA nucleases

    International Nuclear Information System (INIS)

    Kuettner, E. Bartholomeus; Pfeifer, Sven; Keim, Antje; Greiner-Stöffele, Thomas; Sträter, Norbert

    2006-01-01

    Two thermostable DNA nucleases from archaea were crystallized in different space groups; the crystals were suitable for X-ray analysis. Temperature-tolerant organisms are an important source to enhance the stability of enzymes used in biotechnological processes. The DNA-cleaving enzyme exonuclease III from Escherichia coli is used in several applications in gene technology. A thermostable variant could expand the applicability of the enzyme in these methods. Two homologous nucleases from Archaeoglobus fulgidus (ExoAf) and Methanothermobacter thermoautrophicus (ExoMt) were studied for this purpose. Both enzymes were crystallized in different space groups using (poly)ethylene glycols, 2,4-methyl pentandiol, dioxane, ethanol or 2-propanol as precipitants. The addition of a 10-mer DNA oligonucleotide was important to obtain monoclinic crystals of ExoAf and ExoMt that diffracted to resolutions better than 2 Å using synchrotron radiation. The crystal structures of the homologous proteins can serve as templates for genetic engineering of the E. coli exonuclease III and will aid in understanding the different catalytic properties of the enzymes

  19. Insights into the Structures of DNA Damaged by Hydroxyl Radical: Crystal Structures of DNA Duplexes Containing 5-Formyluracil

    Directory of Open Access Journals (Sweden)

    Masaru Tsunoda

    2010-01-01

    Full Text Available Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU, which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.

  20. Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA

    Directory of Open Access Journals (Sweden)

    Yijin Liu

    2015-12-01

    Full Text Available We present the crystal structure of the junction-resolving enzyme GEN1 bound to DNA at 2.5 Å resolution. The structure of the GEN1 protein reveals it to have an elaborated FEN-XPG family fold that is modified for its role in four-way junction resolution. The functional unit in the crystal is a monomer of active GEN1 bound to the product of resolution cleavage, with an extensive DNA binding interface for both helical arms. Within the crystal lattice, a GEN1 dimer interface juxtaposes two products, whereby they can be reconnected into a four-way junction, the structure of which agrees with that determined in solution. The reconnection requires some opening of the DNA structure at the center, in agreement with permanganate probing and 2-aminopurine fluorescence. The structure shows that a relaxation of the DNA structure accompanies cleavage, suggesting how second-strand cleavage is accelerated to ensure productive resolution of the junction.

  1. Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, Chad R.; Zhang, Fei; MacCulloch, Tara; Fahmi, Noureddine; Stephanopoulos, Nicholas; Liu, Yan; Seeman, Nadrian C. [Department; Yan, Hao

    2017-08-02

    The foundational goal of structural DNA nanotechnology—the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems—was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P32 and P31 for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest–DNA conjugates with a specified crystalline hand.

  2. Detection of anthrax lef with DNA-based photonic crystal sensors

    Science.gov (United States)

    Zhang, Bailin; Dallo, Shatha; Peterson, Ralph; Hussain, Syed; Weitao, Tao; Ye, Jing Yong

    2011-12-01

    Bacillus anthracis has posed a threat of becoming biological weapons of mass destruction due to its virulence factors encoded by the plasmid-borne genes, such as lef for lethal factor. We report the development of a fast and sensitive anthrax DNA biosensor based on a photonic crystal structure used in a total-internal-reflection configuration. For the detection of the lef gene, a single-stranded DNA lef probe was biotinylated and immobilized onto the sensor via biotin-streptavidin interactions. A positive control, lef-com, was the complementary strand of the probe, while a negative control was an unrelated single-stranded DNA fragment from the 16S rRNA gene of Acinetobacter baumannii. After addition of the biotinylated lef probe onto the sensor, significant changes in the resonance wavelength of the sensor were observed, resulting from binding of the probe to streptavidin on the sensor. The addition of lef-com led to another significant increase as a result of hybridization between the two DNA strands. The detection sensitivity for the target DNA reached as low as 0.1 nM. In contrast, adding the unrelated DNAs did not cause an obvious shift in the resonant wavelength. These results demonstrate that detection of the anthrax lef by the photonic crystal structure in a total-internal-reflection sensor is highly specific and sensitive.

  3. Enhancement of the fluorescence intensity of DNA intercalators using nano-imprinted 2-dimensional photonic crystal

    International Nuclear Information System (INIS)

    Endo, Tatsuro; Ueda, China; Hisamoto, Hideaki; Kajita, Hiroshi; Okuda, Norimichi; Tanaka, Satoru

    2013-01-01

    We have fabricated polymer-based 2-dimensional photonic crystals that play a key role in enhancing the fluorescence of DNA intercalators. Highly ordered 2-dimensional photonic crystals possessing triangle-shaped and nm-sized hole arrays were fabricated on a 100 μm thick polymer film using nano-imprint lithography. Samples of double-stranded DNAs (sizes: 4361 and 48502 bp; concentration: 1 pM to 10 nM) were adsorbed on the surface of the 2-dimensional photonic crystal by electrostatic interactions and then treated with intercalators. It is found that the fluorescence intensity of the intercalator is enhanced by a factor of up to 10 compared to the enhancement in the absence of the 2-dimensional photonic crystal. Fluorescence intensity increases with increasing length and concentration of the DNAs. If the 2-dimensional photonic crystal is used as a Bragg reflection mirror, the enhancement of fluorescence intensity can be easily observed using a conventional spectrofluorometer. These results suggest that the printed photonic crystal offers a great potential for highly sensitive intercalator-based fluorescent detection of DNAs. (author)

  4. A device that operates within a self-assembled 3D DNA crystal

    Science.gov (United States)

    Hao, Yudong; Kristiansen, Martin; Sha, Ruojie; Birktoft, Jens J.; Hernandez, Carina; Mao, Chengde; Seeman, Nadrian C.

    2017-08-01

    Structural DNA nanotechnology finds applications in numerous areas, but the construction of objects, 2D and 3D crystalline lattices and devices is prominent among them. Each of these components has been developed individually, and most of them have been combined in pairs. However, to date there are no reports of independent devices contained within 3D crystals. Here we report a three-state 3D device whereby we change the colour of the crystals by diffusing strands that contain dyes in or out of the crystals through the mother-liquor component of the system. Each colouring strand is designed to pair with an extended triangle strand by Watson-Crick base pairing. The arm that contains the dyes is quite flexible, but it is possible to establish the presence of the duplex proximal to the triangle by X-ray crystallography. We modelled the transition between the red and blue states through a simple kinetic model.

  5. Ion Density Analysis of Single-Stranded DNA in Liquid Crystal

    Science.gov (United States)

    Iwabata, Kazuki; Seki, Yasutaka; Toizumi, Ryota; Shimada, Yuki; Furue, Hirokazu; Sakaguchi, Kengo

    2013-09-01

    With the widespread use of liquid crystals (LCs) in liquid crystal displays, we have looked into the application of liquid crystals in biotechnology. The purpose of the study described here is to investigate the physical properties of DNA using LCs. Synthetic oligonucleotide molecules were dispersed in MLC6884, the sample injected into antiparallel cells, and the amount of mobile ions was measured. The LC cell doped with oligonucleotide molecules showed a sequence-dependent, specific correlation between oligonucleotide concentration and the amount of mobile ions in the LC cells. In the framework of the Stokes model and polyacrylamide gel electrophoresis (PAGE) analysis, we speculate that this result arises from the difference in ion mobility, which is caused by the shape of the oligonucleotide molecule in the LC.

  6. Quartz microbalance device for transfer into ultrahigh vacuum systems

    International Nuclear Information System (INIS)

    Stavale, F.; Achete, C. A.; Niehus, H.

    2008-01-01

    An uncomplicated quartz microbalance device has been developed which is transferable into ultrahigh vacuum (UHV) systems. The device is extremely useful for flux calibration of different kinds of material evaporators. Mounted on a commercial specimen holder, the device allows fast quartz microbalance transfer into the UHV and subsequent positioning exactly to the sample location where subsequent thin film deposition experiments shall be carried out. After backtransfer into an UHV sample stage, the manipulator may be loaded in situ with the specimen suited for the experiment. The microbalance device capability is demonstrated for monolayer and submonolayer vanadium depositions with an achieved calibration sensitivity of less the 0.001 ML coverage.

  7. Purification, crystallization and preliminary X-ray crystallographic studies of the Mycobacterium tuberculosis DNA gyrase ATPase domain

    International Nuclear Information System (INIS)

    Roué, Mélanie; Agrawal, Alka; Volker, Craig; Mossakowska, Danuta; Mayer, Claudine; Bax, Benjamin D.

    2013-01-01

    The ATPase domain of M. tuberculosis DNA gyrase was crystallized using hanging-drop vapour diffusion. The crystals belonged to space groups P1 and P2 1 . Diffraction data were collected to resolutions of 2.9 and 3.3 Å, respectively. Mycobacterium tuberculosis DNA gyrase, a nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target of fluoroquinolones in the treatment of tuberculosis. The ATPase domain provides the energy required for catalysis by ATP hydrolysis. Two constructs corresponding to this 43 kDa domain, Mtb-GyrB47 C1 and Mtb-GyrB47 C2 , have been overproduced, purified and crystallized. Diffraction data were collected from three crystal forms. The crystals belonged to space groups P1 and P2 1 and diffracted to resolutions of 2.9 and 3.3 Å, respectively

  8. Crystallization and preliminary electron diffraction study to 3. 7 A of DNA helix-destabilizing protein gp32*I

    Energy Technology Data Exchange (ETDEWEB)

    Chiu, W; Hosoda, J

    1978-01-01

    A two-dimensionally large and thin crystal has been obtained from gp32*I, a proteolytically digested product of a DNA helix-destabilizing protein coded by gene 32 in bacteriophage T4. High-resolution electron diffraction patterns (approx. 3.7 A) are recorded from both unstained and stained protein crystals embedded in glucose. The crystal is of orthorhombic space group with a = 62.9 A and b = 47.3 A.

  9. Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog.

    Science.gov (United States)

    Jauch, Ralf; Ng, Calista Keow Leng; Saikatendu, Kumar Singh; Stevens, Raymond C; Kolatkar, Prasanna R

    2008-02-22

    The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as yet unknown mechanism. Here, we report the crystal structure of the murine Nanog homeodomain (HD) and analysis of its interaction with a DNA element derived from the Tcf3 promoter. Two Nanog amino acid pairs, unique among HD sequences, appear to affect the mechanism of nonspecific DNA recognition as well as maintain the integrity of the structural scaffold. To assess selective DNA recognition by Nanog, we performed electrophoretic mobility shift assays using a panel of modified DNA binding sites and found that Nanog HD preferentially binds the TAAT(G/T)(G/T) motif. A series of rational mutagenesis experiments probing the role of six variant residues of Nanog on its DNA binding function establish their role in affecting binding affinity but not binding specificity. Together, the structural and functional evidence establish Nanog as a distant member of a Q50-type HD despite having considerable variation at the sequence level.

  10. Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

    Energy Technology Data Exchange (ETDEWEB)

    Jauch, Ralf; Ng, Calista Keow Leng; Saikatendu, Kumar Singh; Stevens, Raymond C.; Kolatkar, Prasanna R. (GI-Singapore); (Scripps)

    2010-02-08

    The transcription factor Nanog is an upstream regulator in early mammalian development and a key determinant of pluripotency in embryonic stem cells. Nanog binds to promoter elements of hundreds of target genes and regulates their expression by an as yet unknown mechanism. Here, we report the crystal structure of the murine Nanog homeodomain (HD) and analysis of its interaction with a DNA element derived from the Tcf3 promoter. Two Nanog amino acid pairs, unique among HD sequences, appear to affect the mechanism of nonspecific DNA recognition as well as maintain the integrity of the structural scaffold. To assess selective DNA recognition by Nanog, we performed electrophoretic mobility shift assays using a panel of modified DNA binding sites and found that Nanog HD preferentially binds the TAAT(G/T)(G/T) motif. A series of rational mutagenesis experiments probing the role of six variant residues of Nanog on its DNA binding function establish their role in affecting binding affinity but not binding specificity. Together, the structural and functional evidence establish Nanog as a distant member of a Q50-type HD despite having considerable variation at the sequence level.

  11. Quartz crystal microbalance gas sensor with nanocrystalline diamond sensitive layer

    Czech Academy of Sciences Publication Activity Database

    Varga, Marián; Laposa, A.; Kulha, Pavel; Kroutil, J.; Husák, M.; Kromka, Alexander

    2015-01-01

    Roč. 252, č. 11 (2015), s. 2591-2597 ISSN 0370-1972 R&D Projects: GA ČR(CZ) GBP108/12/G108 Institutional support: RVO:68378271 Keywords : gas sensor * nanocrystalline diamond * quartz resonator * thickness shear mode Subject RIV: JB - Sensor s, Measurment, Regulation Impact factor: 1.522, year: 2015

  12. Adsorption and combing of DNA on HOPG surfaces of bulk crystals and nanosheets: application to the bridging of DNA between HOPG/Si heterostructures

    International Nuclear Information System (INIS)

    Rose, F; Martin, P; Fujita, H; Kawakatsu, H

    2006-01-01

    Controlled and reproducible combing of λ-phage DNA molecules can be realized in predetermined orientations on highly oriented pyrolitic graphite (HOPG) surfaces. Observations by atomic force microscopy (AFM) show that DNA adsorption onto HOPG surfaces leads to different hierarchical organizations such as balls, networks, films, and fractal structures. HOPG nanosheets (3.5-100 nm thick) were created by simply rubbing a HOPG crystal onto a silicon oxide surface, and then patterned with a focused ion beam (FIB) to fabricate HOPG/Si heterostructures (arrays of silicon micropillars and microtracks decorated on their top surface with HOPG nanosheets). The surface reactivity of HOPG nanosheets toward DNA is found to be the same as of HOPG bulk crystals. Finally, combing is used to attach and suspend bundles of approximately 20-50 DNA molecules between HOPG/Si heterostructures

  13. Preparation, crystallization and preliminary X-ray diffraction analysis of the DNA-binding domain of the Ets transcription factor in complex with target DNA

    International Nuclear Information System (INIS)

    Suwa, Yoshiaki; Nakamura, Teruya; Toma, Sachiko; Ikemizu, Shinji; Kai, Hirofumi; Yamagata, Yuriko

    2008-01-01

    The complex between the Ets domain of Ets2 and its target DNA has been crystallized. The crystals diffracted to 3.0 Å resolution. The Ets2 transcription factor is a member of the Ets transcription-factor family. Ets2 plays a role in the malignancy of cancer and in Down’s syndrome by regulating the transcription of various genes. The DNA-binding domain of Ets2 (Ets domain; ETSD), which contains residues that are highly conserved among Ets transcription-factor family members, was expressed as a GST-fusion protein. The aggregation of ETSD produced after thrombin cleavage could be prevented by treatment with NDSB-195 (nondetergent sulfobetaine 195). ETSD was crystallized in complex with DNA containing the Ets2 target sequence (GGAA) by the hanging-drop vapour-diffusion method. The best crystals were grown using 25% PEG 3350, 80 mM magnesium acetate, 50 mM sodium cacodylate pH 5.0/5.5 as the reservoir at 293 K. The crystals belonged to space group C2, with unit-cell parameters a = 85.89, b = 95.52, c = 71.89 Å, β = 101.7° and a V M value of 3.56 Å 3 Da −1 . Diffraction data were collected to a resolution of 3.0 Å

  14. Preparation, crystallization and preliminary X-ray diffraction analysis of the DNA-binding domain of the Ets transcription factor in complex with target DNA

    Energy Technology Data Exchange (ETDEWEB)

    Suwa, Yoshiaki; Nakamura, Teruya; Toma, Sachiko; Ikemizu, Shinji; Kai, Hirofumi; Yamagata, Yuriko, E-mail: yamagata@gpo.kumamoto-u.ac.jp [Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973 (Japan)

    2008-03-01

    The complex between the Ets domain of Ets2 and its target DNA has been crystallized. The crystals diffracted to 3.0 Å resolution. The Ets2 transcription factor is a member of the Ets transcription-factor family. Ets2 plays a role in the malignancy of cancer and in Down’s syndrome by regulating the transcription of various genes. The DNA-binding domain of Ets2 (Ets domain; ETSD), which contains residues that are highly conserved among Ets transcription-factor family members, was expressed as a GST-fusion protein. The aggregation of ETSD produced after thrombin cleavage could be prevented by treatment with NDSB-195 (nondetergent sulfobetaine 195). ETSD was crystallized in complex with DNA containing the Ets2 target sequence (GGAA) by the hanging-drop vapour-diffusion method. The best crystals were grown using 25% PEG 3350, 80 mM magnesium acetate, 50 mM sodium cacodylate pH 5.0/5.5 as the reservoir at 293 K. The crystals belonged to space group C2, with unit-cell parameters a = 85.89, b = 95.52, c = 71.89 Å, β = 101.7° and a V{sub M} value of 3.56 Å{sup 3} Da{sup −1}. Diffraction data were collected to a resolution of 3.0 Å.

  15. Crystal structure of Pfu, the high fidelity DNA polymerase from Pyrococcus furiosus.

    Science.gov (United States)

    Kim, Suhng Wook; Kim, Dong-Uk; Kim, Jin Kwang; Kang, Lin-Woo; Cho, Hyun-Soo

    2008-05-01

    We have determined a 2.6A resolution crystal structure of Pfu DNA polymerase, the most commonly used high fidelity PCR enzyme, from Pyrococcus furiosus. Although the structures of Pfu and KOD1 are highly similar, the structure of Pfu elucidates the electron density of the interface between the exonuclease and thumb domains, which has not been previously observed in the KOD1 structure. The interaction of these two domains is known to coordinate the proofreading and polymerization activity of DNA polymerases, especially via H147 that is present within the loop (residues 144-158) of the exonuclease domain. In our structure of Pfu, however, E148 rather than H147 is located at better position to interact with the thumb domain. In addition, the structural analysis of Pfu and KOD1 shows that both the Y-GG/A and beta-hairpin motifs of Pfu are found to differ with that of KOD1, and may explain differences in processivity. This information enables us to better understand the mechanisms of polymerization and proofreading of DNA polymerases.

  16. Purification, crystallization and preliminary X-ray diffraction analysis of the HMG domain of Sox17 in complex with DNA

    International Nuclear Information System (INIS)

    Ng, Calista Keow Leng; Palasingam, Paaventhan; Venkatachalam, Rajakannan; Baburajendran, Nithya; Cheng, Jason; Jauch, Ralf; Kolatkar, Prasanna R.

    2008-01-01

    Crystals of the Sox17 HMG domain bound to LAMA1 enhancer DNA-element crystals that diffracted to 2.75 Å resolution were obtained. Sox17 is a member of the SRY-related high-mobility group (HMG) of transcription factors that have been shown to direct endodermal differentiation in early mammalian development. The LAMA1 gene encoding the α-chain of laminin-1 has been reported to be directly bound and regulated by Sox17. This paper describes the details of initial crystallization attempts with the HMG domain of mouse Sox17 (mSox17-HMG) with a 16-mer DNA element derived from the LAMA1 enhancer and optimization strategies to obtain a better diffracting crystal. The best diffracting crystal was obtained in a condition containing 0.1 M Tris–HCl pH 7.4, 0.2 M MgCl 2 , 30% PEG 3350 using the hanging-drop vapour-diffusion method. A highly redundant in-house data set was collected to 2.75 Å resolution with 99% completeness. The presence of the mSox17-HMG–DNA complex within the crystals was confirmed and Matthews analysis indicated the presence of one complex per asymmetric unit

  17. Crystallization and preliminary X-ray characterization of the eukaryotic replication terminator Reb1-Ter DNA complex.

    Science.gov (United States)

    Jaiswal, Rahul; Singh, Samarendra K; Bastia, Deepak; Escalante, Carlos R

    2015-04-01

    The Reb1 protein from Schizosaccharomyces pombe is a member of a family of proteins that control programmed replication termination and/or transcription termination in eukaryotic cells. These events occur at naturally occurring replication fork barriers (RFBs), where Reb1 binds to termination (Ter) DNA sites and coordinates the polar arrest of replication forks and transcription approaching in opposite directions. The Reb1 DNA-binding and replication-termination domain was expressed in Escherichia coli, purified and crystallized in complex with a 26-mer DNA Ter site. Batch crystallization under oil was required to produce crystals of good quality for data collection. Crystals grew in space group P2₁, with unit-cell parameters a = 68.9, b = 162.9, c = 71.1 Å, β = 94.7°. The crystals diffracted to a resolution of 3.0 Å. The crystals were mosaic and required two or three cycles of annealing. This study is the first to yield structural information about this important family of proteins and will provide insights into the mechanism of replication and transcription termination.

  18. Drinking-Straw Microbalance and Seesaw: Stability and Instability

    Science.gov (United States)

    Chapman, Peter; Glasser, Leslie

    2015-03-01

    The mechanics of a beam balance are little appreciated and seldom understood. We here consider the conditions that result in a stable balance, with center of gravity below the fulcrum (pivot point), while an unstable balance results when the center of gravity is above the fulcrum. The highly sensitive drinking-straw microbalance, which uses a plastic drinking straw as a rigid beam, is briefly described with some slight convenient modifications. Different placements of the center of gravity are considered analytically to explain the equilibrium neutrality, stability, and instability of such beam balances as the microbalance, the playground "seesaw" or "teeter-totter," the "dipping bird," and other toys and magic tricks.

  19. Crystal structure of DNA polymerase III β sliding clamp from Mycobacterium tuberculosis.

    Science.gov (United States)

    Gui, Wen-Jun; Lin, Shi-Qiang; Chen, Yuan-Yuan; Zhang, Xian-En; Bi, Li-Jun; Jiang, Tao

    2011-02-11

    The sliding clamp is a key component of DNA polymerase III (Pol III) required for genome replication. It is known to function with diverse DNA repair proteins and cell cycle-control proteins, making it a potential drug target. To extend our understanding of the structure/function relationship of the sliding clamp, we solved the crystal structure of the sliding clamp from Mycobacterium tuberculosis (M. tuberculosis), a human pathogen that causes most cases of tuberculosis (TB). The sliding clamp from M. tuberculosis forms a ring-shaped head-to-tail dimer with three domains per subunit. Each domain contains two α helices in the inner ring that lie against two β sheets in the outer ring. Previous studies have indicated that many Escherichia coli clamp-binding proteins have a conserved LF sequence, which is critical for binding to the hydrophobic region of the sliding clamp. Here, we analyzed the binding affinities of the M. tuberculosis sliding clamp and peptides derived from the α and δ subunits of Pol III, which indicated that the LF motif also plays an important role in the binding of the α and δ subunits to the sliding clamp of M. tuberculosis. Copyright © 2011 Elsevier Inc. All rights reserved.

  20. Efficient Fluorescence Resonance Energy Transfer between Quantum Dots and Gold Nanoparticles Based on Porous Silicon Photonic Crystal for DNA Detection.

    Science.gov (United States)

    Zhang, Hongyan; Lv, Jie; Jia, Zhenhong

    2017-05-10

    A novel assembled biosensor was prepared for detecting 16S rRNA, a small-size persistent specific for Actinobacteria. The mechanism of the porous silicon (PS) photonic crystal biosensor is based on the fluorescence resonance energy transfer (FRET) between quantum dots (QDs) and gold nanoparticles (AuNPs) through DNA hybridization, where QDs act as an emission donor and AuNPs serve as a fluorescence quencher. Results showed that the photoluminescence (PL) intensity of PS photonic crystal was drastically increased when the QDs-conjugated probe DNA was adhered to the PS layer by surface modification using a standard cross-link chemistry method. The PL intensity of QDs was decreased when the addition of AuNPs-conjugated complementary 16S rRNA was dropped onto QDs-conjugated PS. Based on the analysis of different target DNA concentration, it was found that the decrease of the PL intensity showed a good linear relationship with complementary DNA concentration in a range from 0.25 to 10 μM, and the detection limit was 328.7 nM. Such an optical FRET biosensor functions on PS-based photonic crystal for DNA detection that differs from the traditional FRET, which is used only in liquid. This method will benefit the development of a new optical FRET label-free biosensor on Si substrate and has great potential in biochips based on integrated optical devices.

  1. Micro-ball lens structure fabrication based on drop on demand printing the liquid mold

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Xiaoyang, E-mail: zhuxy1026@163.com; Zhu, Li, E-mail: zhuli@njust.edu.cn; Chen, Hejuan; Yang, Lijun; Zhang, Weiyi

    2016-01-15

    Graphical abstract: - Highlights: • The glycerol micro-ball droplet was introduced to be as liquid mold to fabricate micro-ball lens. • A molding process was used to fabricate the micro-ball lens and the scales of them can be controlled. • The accurate molding process is mainly attributed to the ultrahigh adhesion of the treated substrate. • The micro-ball lenses with contact angle of 120° and 150° were fabricated, analyzed and discussed. - Abstract: In this paper, we demonstrated a simple micro-ball lens array (MBLA) fabrication method using a drop-on-demand (DOD) droplet printing technique and liquid mold. The micro-ball droplet array on the hydrophobic surface is used as the liquid mold to fabricate the MBLA. The ultrahigh adhesion force between the micro-ball droplet and the substrate is ascribed to the Wenzel state of the micro-ball droplet, while the replication process with low position error is attributed to the ultrahigh adhesion force between the micro-ball droplet and the substrate and the high viscosity of the micro-ball droplet and polydimethylsiloxane (PDMS) liquid. The micro-ball lenses (MBLs) with a contact angle of 120° and 150° were fabricated and the important fabrication details were discussed. The optical performance and scanning electron microscope (SEM) data of the MBLs showed that the MBLs had high quality surface morphology and good optical performance.

  2. Mass changes in NSTX Surface Layers with Li Conditioning as Measured by Quartz Microbalances

    International Nuclear Information System (INIS)

    Skinner, C.H.; Kugel, H.W.; Roquemore, A.L.; Krstic, P.S.; Beste, A.

    2008-01-01

    Dynamic retention, lithium deposition, and the stability of thick deposited layers were measured by three quartz crystal microbalances (QMB) deployed in plasma shadowed areas at the upper and lower divertor and outboard midplane in the National Spherical Torus Experiment (NSTX). Deposition of 185 (micro)/g/cm 2 over 3 months in 2007 was measured by a QMB at the lower divertor while a QMB on the upper divertor, that was shadowed from the evaporator, received an order of magnitude less deposition. During helium glow discharge conditioning both neutral gas collisions and the ionization and subsequent drift of Li + interrupted the lithium deposition on the lower divertor. We present calculations of the relevant mean free paths. Occasionally strong variations in the QMB frequency were observed of thick lithium films suggesting relaxation of mechanical stress and/or flaking or peeling of the deposited layers.

  3. Four highly pseudosymmetric and/or twinned structures of d(CGCGCG) 2 extend the repertoire of crystal structures of Z-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Zhipu; Dauter, Zbigniew; Gilski, Miroslaw

    2017-10-30

    DNA oligomer duplexes containing alternating cytosines and guanines in their sequences tend to form left-handed helices of the Z-DNA type, with the sugar and phosphate backbone in a zigzag conformation and a helical repeat of two successive nucleotides. Z-DNA duplexes usually crystallize as hexagonally arranged parallel helical tubes, with various relative orientations and translation of neighboring duplexes. Four novel high-resolution crystal structures of d(CGCGCG)2duplexes are described here. They are characterized by a high degree of pseudosymmetry and/or twinning, with three or four independent duplexes differently oriented in a monoclinicP21lattice of hexagonal metric. The various twinning criteria give somewhat conflicting indications in these complicated cases of crystal pathology. The details of molecular packing in these crystal structures are compared with other known crystal forms of Z-DNA.

  4. Purification, crystallization and preliminary crystallographic analysis of a multiple cofactor-dependent DNA ligase from Sulfophobococcus zilligii

    International Nuclear Information System (INIS)

    Supangat, Supangat; An, Young Jun; Sun, Younguk; Kwon, Suk-Tae; Cha, Sun-Shin

    2010-01-01

    A recombinant multiple cofactor-dependent DNA ligase from S. zilligii has been purified and crystallized. X-ray diffraction data were collected to 2.9 Å resolution and the crystals belonged to space group P1. A recombinant DNA ligase from Sulfophobococcus zilligii that shows multiple cofactor specificity (ATP, ADP and GTP) was expressed in Escherichia coli and purified under reducing conditions. Crystals were obtained by the microbatch crystallization method at 295 K in a drop containing 1 µl protein solution (10 mg ml −1 ) and an equal volume of mother liquor [0.1 M HEPES pH 7.5, 10%(w/v) polyethylene glycol 10 000]. A data set was collected to 2.9 Å resolution using synchrotron radiation. The crystals belonged to space group P1, with unit-cell parameters a = 63.7, b = 77.1, c = 77.8 Å, α = 83.4, β = 82.4, γ = 74.6°. Assuming the presence of two molecules in the unit cell, the solvent content was estimated to be about 53.4%

  5. Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate

    Science.gov (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Muhammad, Niaz; Shah, Naseer Ali; Sohail, Manzar; Pandarinathan, Vedapriya

    2015-08-01

    A new binuclear O-bridged Cu(II) complex with 4-chlorophenyl acetate and 2,2‧-bipyridine has been synthesized and characterized using FT-IR, powder and single crystal XRD and electrochemical solution studies. The results revealed that the two penta-coordinated Cu(II) centers are linked by two carboxylate ligands in end-on bonding fashion. The coordination geometry is slightly distorted square pyramidal (SP) with bridging oxygen atoms occupying the apical position and other ligands lying in the equatorial plane. The striking difference in Cu-O bond distance of the bridging oxygen atom in the complex may be responsible for the SP geometry of Cu(II) ion. The complex gave rise to metal centered irreversible electro-activity where one electron Cu(II)/Cu(III) oxidation process and a single step two electron Cu(II)/Cu(0) reduction process was observed. The redox processes were found predominantly adsorption controlled. The values of diffusion coefficient and heterogeneous rate constant for oxidation process were 6.98 × 10-7 cm2 s-1 and 4.60 × 10-5 cm s-1 while the corresponding values for reduction were 5.30 × 10-8 cm2 s-1 and 5.41 × 10-6 cm s-1, respectively. The formal potential and charge transfer coefficient were also calculated. The DNA-binding ability was explored through cyclic voltammetry and UV-Visible spectroscopy. Diminution in the value of Do for oxidation indicated the binding of the complex with DNA corresponding to Kb = 8.58 × 104 M-1. UV-Visible spectroscopy yielded ε = 49 L mol-1 cm-1 and Kb = 2.96 × 104 M-1. The data of both techniques support each other. The self-induced redox activation of the complex, as indicated by cyclic voltammetry heralds its potential applications in redox catalysis and anticancer activity.

  6. The Crystal Structure of PF-8, the DNA Polymerase Accessory Subunit from Kaposi's Sarcoma-Associated Herpesvirus

    Energy Technology Data Exchange (ETDEWEB)

    Baltz, Jennifer L.; Filman, David J.; Ciustea, Mihai; Silverman, Janice Elaine Y.; Lautenschlager, Catherine L.; Coen, Donald M.; Ricciardi, Robert P.; Hogle, James M.; (UPENN)

    2009-12-01

    Kaposi's sarcoma-associated herpesvirus is an emerging pathogen whose mechanism of replication is poorly understood. PF-8, the presumed processivity factor of Kaposi's sarcoma-associated herpesvirus DNA polymerase, acts in combination with the catalytic subunit, Pol-8, to synthesize viral DNA. We have solved the crystal structure of residues 1 to 304 of PF-8 at a resolution of 2.8 {angstrom}. This structure reveals that each monomer of PF-8 shares a fold common to processivity factors. Like human cytomegalovirus UL44, PF-8 forms a head-to-head dimer in the form of a C clamp, with its concave face containing a number of basic residues that are predicted to be important for DNA binding. However, there are several differences with related proteins, especially in loops that extend from each monomer into the center of the C clamp and in the loops that connect the two subdomains of each protein, which may be important for determining PF-8's mode of binding to DNA and to Pol-8. Using the crystal structures of PF-8, the herpes simplex virus catalytic subunit, and RB69 bacteriophage DNA polymerase in complex with DNA and initial experiments testing the effects of inhibition of PF-8-stimulated DNA synthesis by peptides derived from Pol-8, we suggest a model for how PF-8 might form a ternary complex with Pol-8 and DNA. The structure and the model suggest interesting similarities and differences in how PF-8 functions relative to structurally similar proteins.

  7. The microball and Gammasphere: Research highlights and future directions

    Energy Technology Data Exchange (ETDEWEB)

    Devlin, M.; Sarantites, D.G.; LaFosse, D.R.; Lerma, F. [Washington Univ., Saint Louis, MO (United States)

    1996-12-31

    The Microball, a compact, 4{pi} charged-particle detector array, has been used in conjunction with Gammasphere for numerous physics experiments, and more are planned in the near future. A summary of this research program is presented, and the device and its capabilities are described. An example of its use in the study of the population and entry state excitation energy distributions of normal and superdeformed bands in {sup 82}Sr is presented.

  8. crystal

    Science.gov (United States)

    Yu, Yi; Huang, Yisheng; Zhang, Lizhen; Lin, Zhoubin; Sun, Shijia; Wang, Guofu

    2014-07-01

    A Nd3+:Na2La4(WO4)7 crystal with dimensions of ϕ 17 × 30 mm3 was grown by the Czochralski method. The thermal expansion coefficients of Nd3+:Na2La4(WO4)7 crystal are 1.32 × 10-5 K-1 along c-axis and 1.23 × 10-5 K-1 along a-axis, respectively. The spectroscopic characteristics of Nd3+:Na2La4(WO4)7 crystal were investigated. The Judd-Ofelt theory was applied to calculate the spectral parameters. The absorption cross sections at 805 nm are 2.17 × 10-20 cm2 with a full width at half maximum (FWHM) of 15 nm for π-polarization, and 2.29 × 10-20 cm2 with a FWHM of 14 nm for σ-polarization. The emission cross sections are 3.19 × 10-20 cm2 for σ-polarization and 2.67 × 10-20 cm2 for π-polarization at 1,064 nm. The fluorescence quantum efficiency is 67 %. The quasi-cw laser of Nd3+:Na2La4(WO4)7 crystal was performed. The maximum output power is 80 mW. The slope efficiency is 7.12 %. The results suggest Nd3+:Na2La4(WO4)7 crystal as a promising laser crystal fit for laser diode pumping.

  9. Sharp kink of DNA at psoralen-cross-link site deduced from crystal structure of psoralen-thymine monoadduct

    International Nuclear Information System (INIS)

    Kim, S.H.; Peckler, S.; Graves, B.; Kanne, D.; Rapoport, H.; Hearst, J.E.

    1983-01-01

    Light-induced cross-linking of double-stranded nucleic acids by psoralens has been exploited to locate, in vivo or in vitro, those double-helical regions of DNA or RNA that can accommodate any structural changes caused by the psoralen cross-links. To determine three-dimensional structural parameters of the cross-link, we have solved the crystal structure of the psoralen-thymine monoadduct formed in photoreaction between calf thymus DNA and 8-methoxypsoralen (8MOP). There are eight possible configurations for psoralen-thymine monoadducts and 64 for diadducts. We describe here the structural details of a psoralen-thymine monoadduct obtained in a biological environment and the consequences of the photo-cross-link between 8MOP and double-helical DNA

  10. Crystal Structure of a CRISPR RNA-guided Surveillance Complex Bound to a ssDNA Target

    Energy Technology Data Exchange (ETDEWEB)

    Mulepati, Sabin [Johns Hopkins Univ., Baltimore, MD (United States); Heroux, Annie; Bailey, Scott [Johns Hopkins Univ., Baltimore, MD (United States)

    2014-09-19

    In prokaryotes, RNA derived from type I and type III CRISPR loci direct large ribonucleoprotein complexes to destroy invading bacteriophage and plasmids. In Escherichia coli, this 405-kilodalton complex is called Cascade. We report the crystal structure of Cascade bound to a single-stranded DNA (ssDNA) target at a resolution of 3.03 angstroms. The structure reveals that the CRISPR RNA and target strands do not form a double helix but instead adopt an underwound ribbon-like structure. This noncanonical structure is facilitated by rotation of every sixth nucleotide out of the RNA-DNA hybrid and is stabilized by the highly interlocked organization of protein subunits. These studies provide insight into both the assembly and the activity of this complex and suggest a mechanism to enforce fidelity of target binding.

  11. Purification, crystallization and preliminary X-ray crystallographic analysis of the ETS domain of human Ergp55 in complex with the cfos promoter DNA sequence

    International Nuclear Information System (INIS)

    Gangwar, Shanti P.; Meena, Sita R.; Saxena, Ajay K.

    2012-01-01

    The ETS domain of human Ergp55 was purified and crystallized in native, complexes with E74, and cfos promoter DNA sequences. The X-ray intensity data set was collected on ETS–cfos promoter DNA complex crystal at 3.1 Å resolution to analyze the structure by molecular replacement technique. The Ergp55 protein belongs to the Ets family of transciption factors. The Ets transcription factors are involved in various developmental processes and the regulation of cancer metabolism. They contain a highly similar DNA-binding domain known as the ETS domain and have diverse functions in oncogenesis and physiology. The Ets transcription factors differ in their DNA-binding preference at the ETS site and the mechanisms by which they target genes are not clearly understood. To understand its DNA-binding mechanism, the ETS domain of Ergp55 was expressed and purified. The ETS domain was crystallized in the native form and in complex forms with DNA sequences from the E74 and cfos promoters. An X-ray diffraction data set was collected from an ETS–cfos DNA complex crystal at a wavelength of 0.9725 Å on the BM14 synchrotron beamline at the ESRF, France. The ETS–cfos DNA complex crystal belonged to space group C222 1 , with four molecules in the asymmetric unit. For structure analysis, initial phases for the ETS–cfos DNA complex were obtained by the molecular-replacement technique with Phaser in the CCP4 suite using the coordinates of Fli-1 protein and cfos DNA as search models. Structure analysis of the ETS–cfos DNA complex may possibly explain the DNA-binding specificity and its mechanism of interaction with the ETS domain of Ergp55

  12. Purification, crystallization and preliminary X-ray diffraction experiments on the breakage-reunion domain of the DNA gyrase from Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Piton, Jérémie; Matrat, Stéphanie; Petrella, Stéphanie; Jarlier, Vincent; Aubry, Alexandra; Mayer, Claudine

    2009-01-01

    The breakage-reunion domain of M. tuberculosis DNA gyrase was crystallized using the hanging-drop vapour-diffusion method. One of the four crystal forms obtained belonged to space group C2 and diffraction data were collected to a resolution of 2.7 Å. Mycobacterium tuberculosis DNA gyrase, a nanomachine that is involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target for fluoroquinolone action. The breakage-reunion domain of the A subunit plays an essential role in DNA binding during the catalytic cycle. Two constructs of 53 and 57 kDa (termed GA53BK and GA57BK) corresponding to this domain have been overproduced, purified and crystallized. Diffraction data were collected from four crystal forms. The resolution limits ranged from 4.6 to 2.7 Å depending on the crystal form. The best diffracting crystals belonged to space group C2, with a biological dimer in the asymmetric unit. This is the first report of the crystallization and preliminary X-ray diffraction analysis of the breakage-reunion domain of DNA gyrase from a species containing one unique type II topoisomerase

  13. Crystal Structure of the VapBC Toxin–Antitoxin Complex from Shigella flexneri Reveals a Hetero-Octameric DNA-Binding Assembly

    DEFF Research Database (Denmark)

    Dienemann, Christian; Bøggild, Andreas; Winther, Kristoffer S.

    2011-01-01

    the crystal structure of the intact Shigella flexneri VapBC TA complex, determined to 2.7 Å resolution. Both in solution and in the crystal structure, four molecules of each protein combine to form a large and globular hetero-octameric assembly with SpoVT/AbrB-type DNA-binding domains at each end and a total...

  14. The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.

    Science.gov (United States)

    Jauch, Ralf; Ng, Calista K L; Narasimhan, Kamesh; Kolatkar, Prasanna R

    2012-04-01

    It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

  15. Probing absorption of deuterium into palladium cathodes during D2O electrolysis with an in situ electrochemical microbalance technique

    International Nuclear Information System (INIS)

    Oyama, Noboru; Yamamoto, Nobushige; Hatozaki, Osamu; Ohsaka, Takeo

    1990-01-01

    The in situ observation of the absorption of deuterium (or hydrogen) into the Pd cathode during D 2 O (or H 2 O) electrolysis was made by an electrochemical microbalance technique which is based on the quartz-crystal electrode. The resonant frequency of the Pd-coated quartz-crystal electrode decreased with increasing amount of charge passed during electrolysis, and the frequency change for the D 2 O electrolysis was about twice that for the H 2 O electrolysis. The atom ratios of H/Pd and D/Pd of the H-Pd and D-Pd compounds resulting from the electrolysis were estimated to be 0.59 and 0.57, respectively. (author)

  16. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.

    Science.gov (United States)

    Kouno, Takahide; Silvas, Tania V; Hilbert, Brendan J; Shandilya, Shivender M D; Bohn, Markus F; Kelch, Brian A; Royer, William E; Somasundaran, Mohan; Kurt Yilmaz, Nese; Matsuo, Hiroshi; Schiffer, Celia A

    2017-04-28

    Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.

  17. Crystal structure of the gamma-2 herpesvirus LANA DNA binding domain identifies charged surface residues which impact viral latency.

    Directory of Open Access Journals (Sweden)

    Bruno Correia

    Full Text Available Latency-associated nuclear antigen (LANA mediates γ2-herpesvirus genome persistence and regulates transcription. We describe the crystal structure of the murine gammaherpesvirus-68 LANA C-terminal domain at 2.2 Å resolution. The structure reveals an alpha-beta fold that assembles as a dimer, reminiscent of Epstein-Barr virus EBNA1. A predicted DNA binding surface is present and opposite this interface is a positive electrostatic patch. Targeted DNA recognition substitutions eliminated DNA binding, while certain charged patch mutations reduced bromodomain protein, BRD4, binding. Virus containing LANA abolished for DNA binding was incapable of viable latent infection in mice. Virus with mutations at the charged patch periphery exhibited substantial deficiency in expansion of latent infection, while central region substitutions had little effect. This deficiency was independent of BRD4. These results elucidate the LANA DNA binding domain structure and reveal a unique charged region that exerts a critical role in viral latent infection, likely acting through a host cell protein(s.

  18. Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus

    Energy Technology Data Exchange (ETDEWEB)

    Carr, Stephen B., E-mail: bmbsbc@bmb.leeds.ac.uk [Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (United Kingdom); Makris, George [Omega Mediation Hellas Ltd, Clinical and Pharma Consulting, 11525 N. Psychiko, Athens (Greece); Phillips, Simon E. V.; Thomas, Christopher D. [Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2006-11-01

    The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed. DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-ray analysis revealed that GrlA56 crystals belong to space group P2{sub 1}, diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism.

  19. Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus

    International Nuclear Information System (INIS)

    Carr, Stephen B.; Makris, George; Phillips, Simon E. V.; Thomas, Christopher D.

    2006-01-01

    The crystallization and data collection of topoisomerase IV from S. aureus is described. Phasing by molecular replacement proved difficult owing to the presence of translational NCS and strategies used to overcome this are discussed. DNA topoisomerase IV removes undesirable topological features from DNA molecules in order to help maintain chromosome stability. Two constructs of 56 and 59 kDa spanning the DNA-cleavage domain of the A subunit of topoisomerase IV from Staphylococcus aureus (termed GrlA56 and GrlA59) have been crystallized. Crystals were grown at 291 K using the sitting-drop vapour-diffusion technique with PEG 3350 as a precipitant. Preliminary X-ray analysis revealed that GrlA56 crystals belong to space group P2 1 , diffract to a resolution of 2.9 Å and possess unit-cell parameters a = 83.6, b = 171.5, c = 87.8 Å, β = 90.1°, while crystals of GrlA59 belong to space group P2 1 2 1 2, with unit-cell parameters a = 41.5, b = 171.89, c = 87.9 Å. These crystals diffract to a resolution of 2.8 Å. This is the first report of the crystallization and preliminary X-ray analysis of the DNA-cleavage domain of a topoisomerase IV from a Gram-positive organism

  20. Crystallization and preliminary X-ray analysis of a complex formed between the antibiotic simocyclinone D8 and the DNA breakage–reunion domain of Escherichia coli DNA gyrase

    International Nuclear Information System (INIS)

    Edwards, Marcus J.; Flatman, Ruth H.; Mitchenall, Lesley A.; Stevenson, Clare E. M.; Maxwell, Anthony; Lawson, David M.

    2009-01-01

    Crystals of a complex formed between the 59 kDa N-terminal fragment of the E. coli DNA gyrase A subunit and the antibiotic simocyclinone D8 were obtained and X-ray data were recorded to a resolution of 2.75 Å. Crystals of a complex formed between the 59 kDa N-terminal fragment of the Escherichia coli DNA gyrase A subunit (also known as the breakage–reunion domain) and the antibiotic simocyclinone D8 were grown by vapour diffusion. The complex crystallized with I-centred orthorhombic symmetry and X-ray data were recorded to a resolution of 2.75 Å from a single crystal at the synchrotron. DNA gyrase is an essential bacterial enzyme and thus represents an attractive target for drug development

  1. 40 CFR 92.110 - Weighing chamber and micro-balance.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Weighing chamber and micro-balance. 92... Weighing chamber and micro-balance. (a) Ambient conditions—(1) Temperature. The temperature of the chamber... shall be 45±8 percent during all filter conditioning and weighing. The dew point shall be 6.4 to 12.4 °C...

  2. Direct Atomic Force Microscopy Observation of DNA Tile Crystal Growth at the Single-Molecule Level

    OpenAIRE

    Evans, Constantine G.; Hariadi, Rizal F.; Winfree, Erik

    2012-01-01

    While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detach...

  3. Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level.

    Science.gov (United States)

    Evans, Constantine G; Hariadi, Rizal F; Winfree, Erik

    2012-06-27

    While the theoretical implications of models of DNA tile self-assembly have been extensively researched and such models have been used to design DNA tile systems for use in experiments, there has been little research testing the fundamental assumptions of those models. In this paper, we use direct observation of individual tile attachments and detachments of two DNA tile systems on a mica surface imaged with an atomic force microscope (AFM) to compile statistics of tile attachments and detachments. We show that these statistics fit the widely used kinetic Tile Assembly Model and demonstrate AFM movies as a viable technique for directly investigating DNA tile systems during growth rather than after assembly.

  4. A Histone-Like Protein Induces Plasmid DNA to Form Liquid Crystals in Vitro and Gene Compaction in Vivo

    Directory of Open Access Journals (Sweden)

    Shiyong Sun

    2013-12-01

    Full Text Available The liquid crystalline state is a universal phenomenon involving the formation of an ordered structure via a self-assembly process that has attracted attention from numerous scientists. In this study, the dinoflagellate histone-like protein HCcp3 is shown to induce super-coiled pUC18 plasmid DNA to enter a liquid crystalline state in vitro, and the role of HCcp3 in gene condensation in vivo is also presented. The plasmid DNA (pDNA-HCcp3 complex formed birefringent spherical particles with a semi-crystalline selected area electronic diffraction (SAED pattern. Circular dichroism (CD titrations of pDNA and HCcp3 were performed. Without HCcp3, pUC18 showed the characteristic B conformation. As the HCcp3 concentration increased, the 273 nm band sharply shifted to 282 nm. When the HCcp3 concentration became high, the base pair (bp/dimer ratio fell below 42/1, and the CD spectra of the pDNA-HCcp3 complexes became similar to that of dehydrated A-form DNA. Microscopy results showed that HCcp3 compacted the super-coiled gene into a condensed state and that inclusion bodies were formed. Our results indicated that HCcp3 has significant roles in gene condensation both in vitro and in histone-less eukaryotes in vivo. The present study indicates that HCcp3 has great potential for applications in non-viral gene delivery systems, where HCcp3 may compact genetic material to form liquid crystals.

  5. Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA

    Energy Technology Data Exchange (ETDEWEB)

    R Jauch; S Choo; C Ng; P Kolatkar

    2011-12-31

    POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.

  6. Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs.

    Science.gov (United States)

    Kondo, Jiro; Yamada, Tom; Hirose, Chika; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

    2014-02-24

    The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States

    Energy Technology Data Exchange (ETDEWEB)

    Dolan, Kyle T.; Duguid, Erica M.; He, Chuan (UC)

    2011-11-17

    SlyA is a master virulence regulator that controls the transcription of numerous genes in Salmonella enterica. We present here crystal structures of SlyA by itself and bound to a high-affinity DNA operator sequence in the slyA gene. SlyA interacts with DNA through direct recognition of a guanine base by Arg-65, as well as interactions between conserved Arg-86 and the minor groove and a large network of non-base-specific contacts with the sugar phosphate backbone. Our structures, together with an unpublished structure of SlyA bound to the small molecule effector salicylate (Protein Data Bank code 3DEU), reveal that, unlike many other MarR family proteins, SlyA dissociates from DNA without large conformational changes when bound to this effector. We propose that SlyA and other MarR global regulators rely more on indirect readout of DNA sequence to exert control over many genes, in contrast to proteins (such as OhrR) that recognize a single operator.

  8. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the central zinc-binding domain of the human Mcm10 DNA-replication factor

    International Nuclear Information System (INIS)

    Jung, Nam Young; Bae, Won Jin; Chang, Jeong Ho; Kim, Young Chang; Cho, Yunje

    2008-01-01

    Mcm10 is a highly conserved nuclear protein that plays a key role in the initiation and elongation processes of DNA replication by providing a physical link between the Mcm2–7 complex and DNA polymerases. In this study, the central domain of human Mcm10 was crystallized using the hanging-drop vapour-diffusion method in the presence of PEG 3350. The initiation of eukaryotic DNA replication requires the tightly controlled assembly of a set of replication factors. Mcm10 is a highly conserved nuclear protein that plays a key role in the initiation and elongation processes of DNA replication by providing a physical link between the Mcm2–7 complex and DNA polymerases. The central domain, which contains the CCCH zinc-binding motif, is most conserved within Mcm10 and binds to DNA and several proteins, including proliferative cell nuclear antigen. In this study, the central domain of human Mcm10 was crystallized using the hanging-drop vapour-diffusion method in the presence of PEG 3350. An X-ray diffraction data set was collected to a resolution of 2.6 Å on a synchrotron beamline. The crystals formed belonged to space group R3, with unit-cell parameters a = b = 99.5, c = 133.0 Å. According to Matthews coefficient calculations, the crystals were predicted to contain six MCM10 central domain molecules in the asymmetric unit

  9. Synthesis, characterization, crystal structure and theoretical study of a compound with benzodiazole ring: antimicrobial activity and DNA binding.

    Science.gov (United States)

    Latha, P; Kodisundaram, P; Sundararajan, M L; Jeyakumar, T

    2014-08-14

    2-(Thiophen-2-yl)-1-((thiophen-2-yl)methyl)-1H-1,3-benzodiazole (HL) is synthesized and characterized by elemental analysis, UV-Vis, FT-IR, (1)H, (13)C NMR, mass spectra, scanning electron microscope (SEM) and single crystal X-ray diffraction. The crystal structure is stabilized by intermolecular CH⋯N and CH⋯π interactions. The molecular structure is also optimized at the B3LYP/6-31G level using density functional theory (DFT). The structural parameters from the theory are nearer to those of crystal, the calculated total energy of coordination is -1522.814a.u. The energy of HOMO-LUMO and the energy gap are -0.20718, -0.04314, 0.16404a.u, respectively. All data obtained from the spectral studies support the structural properties of the compound HL. The benzimidazole ring is essentially planar. The in vitro biological screening effects of the synthesized compound is tested against four bacterial and four fungal strains by well diffusion method. Antioxidant property and DNA binding behaviour of the compound has been investigated using spectrophotometric method. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Cockayne syndrome protein A in complex with DNA damage-binding protein 1

    International Nuclear Information System (INIS)

    Meulenbroek, Elisabeth M.; Pannu, Navraj S.

    2011-01-01

    Human Cockayne syndrome protein A has been cocrystallized with human DNA damage-binding protein 1 and data have been collected to 2.9 Å resolution. Cockayne syndrome protein A is one of the main components in mammalian transcription coupled repair. Here, the overproduction, purification and crystallization of human Cockayne syndrome protein A in complex with its interacting partner DNA damage binding protein 1 are reported. The complex was coproduced in insect cells, copurified and crystallized using sitting drops with PEG 3350 and sodium citrate as crystallizing agents. The crystals had unit-cell parameters a = b = 142.03, c = 250.19 Å and diffracted to 2.9 Å resolution on beamline ID14-1 at the European Synchrotron Radiation Facility

  11. Crystallization and preliminary crystallographic analysis of the transcriptional regulator RfaH from Escherichia coli and its complex with ops DNA

    International Nuclear Information System (INIS)

    Vassylyeva, Marina N.; Svetlov, Vladimir; Klyuyev, Sergiy; Devedjiev, Yancho D.; Artsimovitch, Irina; Vassylyev, Dmitry G.

    2006-01-01

    The E. coli transcriptional regulator RfaH was cloned, expressed, purified and crystallized and the complex of RfaH with its target DNA oligonucleotide was cocrystallized. Complete diffraction data sets were collected for the apo protein and its nucleic acid complex at 2.4 and at 1.6 Å resolution, respectively. The bacterial transcriptional factor and virulence regulator RfaH binds to rapidly moving transcription elongation complexes through specific interactions with the exposed segment of the non-template DNA strand. To elucidate this unusual mechanism of recruitment, determination of the three-dimensional structure of RfaH and its complex with DNA was initiated. To this end, the Escherichia coli rfaH gene was cloned and expressed. The purified protein was crystallized by the sitting-drop vapor-diffusion technique. The space group was P6 1 22 or P6 5 22, with unit-cell parameters a = b = 45.46, c = 599.93 Å. A complex of RfaH and a nine-nucleotide oligodeoxyribonucleotide was crystallized by the same technique, but under different crystallization conditions, yielding crystals that belonged to space group P1 (unit-cell parameters a = 36.79, b = 44.01, c = 62.37 Å, α = 80.62, β = 75.37, γ = 75.41°). Complete diffraction data sets were collected for RfaH and its complex with DNA at 2.4 and 1.6 Å resolution, respectively. Crystals of selenomethionine-labeled proteins in both crystal forms were obtained by cross-microseeding using the native microcrystals. The structure determination of RfaH and its complex with DNA is in progress

  12. DNA hosted and aligned in aqueous interstitia of a lamellar liquid crystal – a membrane–biomacromolecule interaction model system

    KAUST Repository

    Carlsson, Nils; Jonsson, Fabian; Wilhelmsson, L. Marcus; Nordé n, Bengt; Å kerman, Bjö rn

    2013-01-01

    We report that DNA molecules can be intercalated and macroscopically oriented in the aqueous interstitia of a lyotropic lamellar liquid crystal. Using UV-vis linear dichroism and fluorescence spectroscopy we show that double-stranded oligonucleotides (25 base pairs) in the water-octanoate-decanol system remain base-paired in the B conformation and are confined in two dimensions, with the helix axis preferentially parallel to the lipid bilayer surfaces but free to rotate within this plane. The degree of helix confinement and the corresponding 2-D orientation can be improved by decreasing the thickness of the water interstitia via the fraction of water in the ternary mixture. Not surprisingly, the corresponding single-stranded oligonucleotides are not aligned, with their persistence length being short in comparison to the lamellar interstitium thickness. We propose this as a model system for studying interactions of DNA-ligand complexes near a lipid bilayer membrane which we demonstrate by using dye probes that are either covalently attached to one end of the oligonucleotide or reversibly bound by intercalation between the base pairs. Three cationic dyes, all strongly bound by intercalation to DNA when free in solution, are found to not bind to DNA but to prefer the membrane surface. The covalently attached Cy5 also binds to the bilayer while Cy3 tends to end-stack to the oligonucleotide duplex. The orientation of Cy5 parallel to the membrane indicates that electrostatic surface binding predominates over insertion into the hydrophobic interior of the membrane. Anionic and zwitterionic dyes (FAM and ROX) are found to remain randomly oriented in the water between the lipid bilayer surfaces. © The Royal Society of Chemistry.

  13. DNA binding by the plant-specific NAC transcription factors in crystal and solution

    DEFF Research Database (Denmark)

    Welner, Ditte Hededam; Lindemose, Søren; Grossmann, J. Günter

    2012-01-01

    angle X-ray scattering on complexes with oligonucleotides, mutagenesis and (DNase I and uranyl photo-) footprinting, is combined to form a structural view of DNA-binding, and for the first time provide experimental evidence for the speculated relationship between plant-specific NAC proteins, WRKY...

  14. An asymmetric resonant coupling wireless power transmission link for Micro-Ball Endoscopy.

    Science.gov (United States)

    Sun, Tianjia; Xie, Xiang; Li, Guolin; Gu, Yingke; Deng, Yangdong; Wang, Ziqiang; Wang, Zhihua

    2010-01-01

    This paper investigates the design and optimization of a wireless power transmission link targeting Micro-Ball Endoscopy applications. A novel asymmetric resonant coupling structure is proposed to deliver power to an endoscopic Micro-Ball system for image read-out after it is excreted. Such a technology enables many key medical applications with stringent requirements for small system volume and high power delivery efficiency. A prototyping power transmission sub-system of the Micro-Ball system was implemented. It consists of primary coil, middle resonant coil, and cube-like full-direction secondary receiving coils. Our experimental results proved that 200mW of power can be successfully delivered. Such a wireless power transmission capability could satisfy the requirements of the Micro-Ball based endoscopy application. The transmission efficiency is in the range of 41% (worst working condition) to 53% (best working condition). Comparing to conventional structures, Asymmetric Resonant Coupling Structure improves power efficiency by 13%.

  15. In situ X-ray data collection from highly sensitive crystals of Pseudomonas putida PtxS in complex with DNA

    International Nuclear Information System (INIS)

    Pineda-Molina, E.; Daddaoua, A.; Krell, T.; Ramos, J. L.; García-Ruiz, J. M.; Gavira, J. A.

    2012-01-01

    The crystallization of both native P. putida transcriptional regulator PtxS and its complex with its DNA recognition sequence using the counter-diffusion method are reported. Pseudomonas putida PtxS is a member of the LacI protein family of transcriptional regulators involved in glucose metabolism. All genes involved in this pathway are clustered into two operons, kgu and gad. PtxS controls the expression of the kgu and gad operons as well as its own transcription. The PtxS operator is a perfect palindrome, 5′-TGAAACCGGTTTCA-3′, which is present in all three promoters. Crystallization of native PtxS failed, and PtxS–DNA crystals were finally produced by the counter-diffusion technique. A portion of the capillary used for crystal growth was attached to the end of a SPINE standard cap and directly flash-cooled in liquid nitrogen for diffraction tests. A full data set was collected with a beam size of 10 × 10 µm. The crystal belonged to the trigonal space group P3, with unit-cell parameters a = b = 213.71, c = 71.57 Å. Only unhandled crystals grown in capillaries of 0.1 mm inner diameter diffracted X-rays to 1.92 Å resolution

  16. A mononuclear zinc(II) complex with piroxicam: Crystal structure, DNA- and BSA-binding studies; in vitro cell cytotoxicity and molecular modeling of oxicam complexes

    Science.gov (United States)

    Jannesari, Zahra; Hadadzadeh, Hassan; Amirghofran, Zahra; Simpson, Jim; Khayamian, Taghi; Maleki, Batool

    2015-02-01

    A new mononuclear Zn(II) complex, trans-[Zn(Pir)2(DMSO)2], where Pir- is 4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (piroxicam), has been synthesized and characterized. The crystal structure of the complex was obtained by the single crystal X-ray diffraction technique. The interaction of the complex with DNA and BSA was investigated. The complex interacts with FS-DNA by two binding modes, viz., electrostatic and groove binding (major and minor). The microenvironment and the secondary structure of BSA are changed in the presence of the complex. The anticancer effects of the seven complexes of oxicam family were also determined on the human K562 cell lines and the results showed reasonable cytotoxicities. The interactions of the oxicam complexes with BSA and DNA were modeled by molecular docking and molecular dynamic simulation methods.

  17. Caesium releases under the form of silicon micro-balls during the Fukushima-Daiichi accident. Information note

    International Nuclear Information System (INIS)

    2016-01-01

    After having outlined that the most part (89 per cent) of radioactive cesium released in the atmosphere during the Fukushima accident was made under the form of silicon micro-balls which were more irradiating than other aerosols marked by cesium radioactive isotopes, this note first discusses whether these silicon micro-balls containing radioactive cesium were resulting from a specific phase of atmospheric release. It discusses the nature of these micro-balls, and discusses whether it is possible to quantitatively assess the contribution of these micro-balls to global releases and deposits. It discusses how these micro-balls could have formed, whether their formation can be associated with a specific phase of reactor degradation or with the degradation of a specific reactor. It discusses whether a specific behaviour of these micro-balls can be expected in the environment, and their possible impacts on radiological consequences

  18. Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA element

    International Nuclear Information System (INIS)

    Baburajendran, Nithya; Palasingam, Paaventhan; Ng, Calista Keow Leng; Jauch, Ralf; Kolatkar, Prasanna R.

    2009-01-01

    Crystals of palindromic SBE DNA-bound Smad1 MH1 domain diffracting to 2.7 Å resolution have been obtained. The bone morphogenetic protein (BMP) signalling pathway regulates diverse processes such as cell differentiation, anterior/posterior axis specification, cell growth and the formation of extra-embryonic tissues. The transcription factor Smad1 relays the BMP signal from the cytoplasm to the nucleus, where it binds short DNA-sequence motifs and regulates gene expression. However, how Smad1 selectively targets particular genomic regions is poorly understood. In order to understand the physical basis of the specific interaction of Smad1 with DNA and to contrast it with the highly homologous but functionally distinct Smad3 protein, the DNA-binding Mad-homology 1 (MH1) domain of Smad1 was cocrystallized with a 17-mer palindromic Smad-binding element (SBE). The extensive optimizations of the length, binding-site spacing and terminal sequences of the DNA element in combination with the other crystallization parameters necessary for obtaining diffraction-quality crystals are described here. A 2.7 Å resolution native data set was collected at the National Synchrotron Radiation Research Centre, Taiwan, from crystals grown in a solution containing 0.2 M ammonium tartrate dibasic, 20% PEG 3350, 3% 2-propanol and 10% glycerol. The data set was indexed and merged in space group P222, with unit-cell parameters a = 73.94, b = 77.49, c = 83.78 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of two Smad1 MH1 molecules bound to the duplex DNA in the asymmetric unit

  19. Post mortem analysis of a JET quartz microbalance system

    Energy Technology Data Exchange (ETDEWEB)

    Esser, H.G. [Association EURATOM-Forschungszentrum Juelich, IPP, D-52425, Juelich (Germany)]. E-mail: h.g.esser@fz-juelich.de; Philipps, V. [Association EURATOM-Forschungszentrum Juelich, IPP, D-52425, Juelich (Germany); Wienhold, P. [Association EURATOM-Forschungszentrum Juelich, IPP, D-52425, Juelich (Germany); Sugiyama, K. [Department of Nuclear Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Kreter, A. [Association EURATOM-Forschungszentrum Juelich, IPP, D-52425, Juelich (Germany); Coad, J.P. [UKAEA/EURATOM Fusion Association, Culham Science Centre, Abingdon (United Kingdom); Tanabe, T. [Department of Nuclear Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)

    2007-06-15

    In the year 2001, a quartz microbalance system (QMB) was installed in the remote area of the inner JET divertor to investigate in situ material erosion and redeposition processes. When removed in 2004, the system was found to be coated all over with carbon deposits. The deposit on the quartz oscillator and the outer and inner housing was analysed by various methods, as SIMS (secondary ion mass spectroscopy), stylus depth profilometry, EPMA (electron probe microanalysis), TIPT (Tritium imaging plate technique) and colorimetry and compared to the frequency change of the quartz. The layer thickness was determined to 1.85 {+-} 0.1 {mu}m in average on an area of 0.95 cm{sup 2} which has to be related to the equivalent of 1.77 x 10{sup -4} g measured from the frequency change of 23 640 Hz. This corresponds to a carbon areal density of 9.3 x 10{sup 18} C atoms/cm{sup 2}. Significant deposition was found also on the surfaces inside the QMB housing which can only be understood if reflection and low sticking is assumed for a high fraction of particles.

  20. Quartz Microbalance Sensor for the Detection of Acrylamide

    Directory of Open Access Journals (Sweden)

    Christoph A. Schalley

    2004-10-01

    Full Text Available Abstract: Several macrocycles of the Hunter-Vögtle type have been identified as superior host compounds for the detection of small amounts of acrylamide. When coated onto the surface of a quartz microbalance, these compounds serve as highly sensitive and selective sensor-active layers for their use in electronic noses. In this study, differently substituted macrocycles were investigated including an open-chain analogue and a catenane. Their structure and functional groups are correlated with their observed affinities to acrylamide and related acids and amides. The much smaller response of the open-chain compound and the almost absent sensor response of the catenane suggest that binding occurs within the cavity of the macrocycle. Theoretical calculations agree well with the experimental data even though they do not yet take into account the arrangement of the macrocycles in the sensor-active layer. The lower detection limit of acrylamide is 10 parts per billion (ppb, which is impressively low for this type of sensor. Other related compounds such as acrylic acid, propionamide, or propionic acid show no or significantly lower affinities to the macrocycles in these concentration ranges.

  1. Influence of Proton and Salt Concentration on the Chromonic Liquid Crystal Phase Diagram of Disodium Cromoglycate Solutions: Prospects and Limitations of a Host for DNA Nanostructures.

    Science.gov (United States)

    Zhang, Bingru; Kitzerow, Heinz-S

    2016-03-31

    Lyotropic chromonic liquid crystals have recently been suggested for use as a self-organized host for dispersing and aligning self-organized DNA origami nanostructures. However, an appropriate pH value and a suitable cation concentration are necessary to stabilize such nanostructures and to avoid unfolding of the DNA. The present study shows that the nematic and columnar liquid crystal phases appearing in aqueous solutions of disodium cromoglycate are robust against the replacement of deionized water by a neutral or alkaline buffer solution. However, disodium cromoglycate precipitates when an acidic buffer is used or when the concentration of magnesium cations exceeds a critical concentration of about 0.6-0.7 mmol/L.

  2. Development of a high-pressure microbalance for hydrogen storage materials

    DEFF Research Database (Denmark)

    Vestbø, Andreas Peter; Jensen, Jens Oluf; Bjerrum, Niels

    2007-01-01

    Pressure-composition isotherms (PCI's) help to determine thermodynamic properties related to hydrogen uptake of materials. PCI's are normally obtained volumetrically with a Sieverts type apparatus or gravimetrically with a microbalance. A potential problem with the gravimetric technique is that t......Pressure-composition isotherms (PCI's) help to determine thermodynamic properties related to hydrogen uptake of materials. PCI's are normally obtained volumetrically with a Sieverts type apparatus or gravimetrically with a microbalance. A potential problem with the gravimetric technique...... of an electromagnetic microbalance, pressure resistant casing for up to 100 bar hydrogen, a flow system for hydrogen and inert gas, heating elements for temperature control, and software for controlling the system. Thermal convection effects are observed and dampened by heating on both the sample and a counterweight...

  3. Integration of the Self-Healing eDNA Architecture in a Liquid Crystal Waveguide-based Fourier Transform Spectrometer

    DEFF Research Database (Denmark)

    Boesen, Michael Reibel; Keymeulen, D.; Madsen, Jan

    2011-01-01

    In this work we describe the first real world case study for the self-healing eDNA (electronic DNA) architecture by implementing the control and data processing of a Fourier Transform Spectrometer (FTS) on an eDNA prototype. For this purpose the eDNA prototype has been ported from a Xilinx Virtex 5...

  4. Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA element

    Science.gov (United States)

    Baburajendran, Nithya; Palasingam, Paaventhan; Ng, Calista Keow Leng; Jauch, Ralf; Kolatkar, Prasanna R.

    2009-01-01

    The bone morphogenetic protein (BMP) signalling pathway regulates diverse processes such as cell differentiation, anterior/posterior axis specification, cell growth and the formation of extra-embryonic tissues. The transcription factor Smad1 relays the BMP signal from the cytoplasm to the nucleus, where it binds short DNA-sequence motifs and regulates gene expression. However, how Smad1 selectively targets particular genomic regions is poorly understood. In order to understand the physical basis of the specific interaction of Smad1 with DNA and to contrast it with the highly homologous but functionally distinct Smad3 protein, the DNA-binding Mad-homology 1 (MH1) domain of Smad1 was cocrystallized with a 17-mer palindromic Smad-binding element (SBE). The extensive optimizations of the length, binding-site spacing and terminal sequences of the DNA element in combination with the other crystallization parameters necessary for obtaining diffraction-quality crystals are described here. A 2.7 Å resolution native data set was collected at the National Synchrotron Radiation Research Centre, Taiwan, from crystals grown in a solution containing 0.2 M ammonium tartrate dibasic, 20% PEG 3350, 3% 2-­propanol and 10% glycerol. The data set was indexed and merged in space group P222, with unit-cell parameters a = 73.94, b = 77.49, c = 83.78 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of two Smad1 MH1 molecules bound to the duplex DNA in the asymmetric unit. PMID:19923727

  5. Mutation and crystallization of the first KH domain of human polycytosine-binding protein 1 (PCBP1) in complex with DNA

    International Nuclear Information System (INIS)

    Yoga, Yano M. K.; Traore, Daouda A. K.; Wilce, Jacqueline A.; Wilce, Matthew C. J.

    2011-01-01

    The successful preparation of a mutant KH domain representing the first KH domain of PCBP1 and its crystallization in complex with a C-rich DNA are reported. This structure is anticipated to provide high-resolution information that will allow better understanding of the basis of cytosine specificity by PCBPs. Polycytosine-binding proteins (PCBPs) are triple KH-domain proteins that play an important role in the regulation of translation of eukaryotic mRNA. They are also utilized by viral RNA and have been shown to interact with ssDNA. Underlying their function is the specific recognition of C-rich nucleotides by their KH domains. However, the structural basis of this recognition is only partially understood. Here, the preparation of a His-tagged KH domain is described, representing the first domain of PCBP1 that incorporates a C54S mutation as well as the addition of a C-terminal tryptophan. This construct has facilitated the preparation of highly diffracting crystals in complex with C-rich DNA (sequence ACCCCA). Crystals of the KH1–DNA complex were grown using the hanging-drop vapour-diffusion method in 0.1 M phosphate–citrate pH 4.2, 40%(v/v) PEG 300. X-ray diffraction data were collected to 1.77 Å resolution and the diffraction was consistent with space group P2 1 , with unit-cell parameters a = 38.59, b = 111.88, c = 43.42 Å, α = γ = 90.0, β = 93.37°. The structure of the KH1–DNA complex will further our insight into the basis of cytosine specificity by PCBPs

  6. Reversible assembly of protein-DNA nanostructures triggered by mediated electron transfer

    International Nuclear Information System (INIS)

    Vogt, Stephan; Wenderhold-Reeb, Sabine; Nöll, Gilbert

    2017-01-01

    Stable protein-DNA nanostructures have been assembled by reconstitution of the multi-ligand binding flavoprotein dodecin on top of flavin-terminated dsDNA monolayers on gold electrodes. These structures could be disassembled by electrochemical flavin reduction via mediated electron transfer. For this purpose a negative potential was applied at the Au working electrode in the presence of the redox mediator bis-(ammoniumethyl)-4,4′-bipyridinium tetrabromide. The stepwise formation of the flavin-terminated dsDNA monolayers as well as the binding and electrochemically triggered release of apododecin were monitored by surface plasmon resonance (SPR) and quartz crystal microbalance (QCM) measurements. The assembly and disassembly of the protein-DNA nanostructures were fully reversible processes, which could be carried out multiple times at the same flavin-dsDNA modified surface. When a negative potential was applied in the absence of a redox mediator apododecin could not be released, i.e. direct electron transfer was not possible. As alternative redox mediators also methylene blue and phenosafranine were studied, but in the presence of these molecules apododecin was released without applying a potential, probably because the tricyclic aromatic compounds are able to replace the flavins at the binding sites.

  7. Crystal Structure of Mycobacterium tuberculosis H37Rv AldR (Rv2779c), a Regulator of the ald Gene: DNA BINDING AND IDENTIFICATION OF SMALL MOLECULE INHIBITORS.

    Science.gov (United States)

    Dey, Abhishek; Shree, Sonal; Pandey, Sarvesh Kumar; Tripathi, Rama Pati; Ramachandran, Ravishankar

    2016-06-03

    Here we report the crystal structure of M. tuberculosis AldR (Rv2779c) showing that the N-terminal DNA-binding domains are swapped, forming a dimer, and four dimers are assembled into an octamer through crystal symmetry. The C-terminal domain is involved in oligomeric interactions that stabilize the oligomer, and it contains the effector-binding sites. The latter sites are 30-60% larger compared with homologs like MtbFFRP (Rv3291c) and can consequently accommodate larger molecules. MtbAldR binds to the region upstream to the ald gene that is highly up-regulated in nutrient-starved tuberculosis models and codes for l-alanine dehydrogenase (MtbAld; Rv2780). Further, the MtbAldR-DNA complex is inhibited upon binding of Ala, Tyr, Trp and Asp to the protein. Studies involving a ligand-binding site G131T mutant show that the mutant forms a DNA complex that cannot be inhibited by adding the amino acids. Comparative studies suggest that binding of the amino acids changes the relative spatial disposition of the DNA-binding domains and thereby disrupt the protein-DNA complex. Finally, we identified small molecules, including a tetrahydroquinoline carbonitrile derivative (S010-0261), that inhibit the MtbAldR-DNA complex. The latter molecules represent the very first inhibitors of a feast/famine regulatory protein from any source and set the stage for exploring MtbAldR as a potential anti-tuberculosis target. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Sensing Conformational Changes in DNA upon Ligand Binding Using QCM-D. Polyamine Condensation and Rad51 Extension of DNA Layers

    KAUST Repository

    Sun, Lu

    2014-10-16

    © 2014 American Chemical Society. Biosensors, in which binding of ligands is detected through changes in the optical or electrochemical properties of a DNA layer confined to the sensor surface, are important tools for investigating DNA interactions. Here, we investigate if conformational changes induced in surface-attached DNA molecules upon ligand binding can be monitored by the quartz crystal microbalance with dissipation (QCM-D) technique. DNA duplexes containing 59-184 base pairs were formed on QCM-D crystals by stepwise assembly of synthetic oligonucleotides of designed base sequences. The DNA films were exposed to the cationic polyamines spermidine and spermine, known to condense DNA molecules in bulk experiments, or to the recombination protein Rad51, known to extend the DNA helix. The binding and dissociation of the ligands to the DNA films were monitored in real time by measurements of the shifts in resonance frequency (Δf) and in dissipation (ΔD). The QCM-D data were analyzed using a Voigt-based model for the viscoelastic properties of polymer films in order to evaluate how the ligands affect thickness and shear viscosity of the DNA layer. Binding of spermine shrinks all DNA layers and increases their viscosity in a reversible fashion, and so does spermidine, but to a smaller extent, in agreement with its lower positive charge. SPR was used to measure the amount of bound polyamines, and when combined with QCM-D, the data indicate that the layer condensation leads to a small release of water from the highly hydrated DNA films. The binding of Rad51 increases the effective layer thickness of a 59bp film, more than expected from the know 50% DNA helix extension. The combined results provide guidelines for a QCM-D biosensor based on ligand-induced structural changes in DNA films. The QCM-D approach provides high discrimination between ligands affecting the thickness and the structural properties of the DNA layer differently. The reversibility of the film

  9. Conformational and mechanical changes of DNA upon transcription factor binding detected by a QCM and transmission line model.

    Science.gov (United States)

    de-Carvalho, Jorge; Rodrigues, Rogério M M; Tomé, Brigitte; Henriques, Sílvia F; Mira, Nuno P; Sá-Correia, Isabel; Ferreira, Guilherme N M

    2014-04-21

    A novel quartz crystal microbalance (QCM) analytical method is developed based on the transmission line model (TLM) algorithm to analyze the binding of transcription factors (TFs) to immobilized DNA oligoduplexes. The method is used to characterize the mechanical properties of biological films through the estimation of the film dynamic shear moduli, G and G, and the film thickness. Using the Saccharomyces cerevisiae transcription factor Haa1 (Haa1DBD) as a biological model two sensors were prepared by immobilizing DNA oligoduplexes, one containing the Haa1 recognition element (HRE(wt)) and another with a random sequence (HRE(neg)) used as a negative control. The immobilization of DNA oligoduplexes was followed in real time and we show that DNA strands initially adsorb with low or non-tilting, laying flat close to the surface, which then lift-off the surface leading to final film tilting angles of 62.9° and 46.7° for HRE(wt) and HRE(neg), respectively. Furthermore we show that the binding of Haa1DBD to HRE(wt) leads to a more ordered and compact film, and forces a 31.7° bending of the immobilized HRE(wt) oligoduplex. This work demonstrates the suitability of the QCM to monitor the specific binding of TFs to immobilized DNA sequences and provides an analytical methodology to study protein-DNA biophysics and kinetics.

  10. Waveguide-coupled micro-ball lens array suitable for mass fabrication

    NARCIS (Netherlands)

    Chang, Lantian; Dijkstra, Meindert; Ismail, Nur; Pollnau, Markus; de Ridder, René M; Wörhoff, Kerstin; Subramaniam, Vinod; Kanger, Johannes S

    2015-01-01

    We demonstrate a fabrication procedure for the direct integration of micro-ball lenses on planar integrated optical channel waveguide chips with the aim to reduce the divergence of light that arises from the waveguide in both horizontal and vertical directions. Fabrication of the lenses is based on

  11. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  12. The stability of PEMFC electrodes : platinum dissolution vs potential and temperature investigated by quartz crystal microbalance

    NARCIS (Netherlands)

    Dam, V.A.T.; Bruijn, de F.A.

    2007-01-01

    The stability of platinum in proton exchange membrane fuel cell (PEMFC) electrodes has been investigated by determining the dissolution of platinum from a thin platinum film deposited on a gold substrate in 1 M HClO4 at different temperatures ranging between 40 and 80°C and potentials between 0.85

  13. Determination of the dopant weight fraction in polyaniline films using a quartz-crystal microbalance

    Czech Academy of Sciences Publication Activity Database

    Ayad, M. M.; Zaki, E. A.; Stejskal, Jaroslav

    2007-01-01

    Roč. 515, č. 23 (2007), s. 8381-8385 ISSN 0040-6090 R&D Projects: GA AV ČR IAA4050313 Institutional research plan: CEZ:AV0Z40500505 Keywords : dopant weight fraction * polyaniline * polyaniline film Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.693, year: 2007

  14. Application of an Electrochemical Quartz Crystal Microbalance to the study of electrocatalytic films

    Energy Technology Data Exchange (ETDEWEB)

    Gordon, Jr., James S. [Iowa State Univ., Ames, IA (United States)

    1993-09-01

    The EQCM was used to study the deposition and composition of electrodeposited pure PbO2 and Bi-doped PbO2 active toward anodic oxygen-transfer reactions. Within the doped films, Bi is incorporated as Bi+5 in the form of BiO2A, where A is ClO4- or NO3-. For deposition of these 2 materials, changes in hydration between the Au oxide and the depositing film resulted in higher mass-to-charge ratios. XRD and XPS were used to study the films; the rutile structure of PbO2 is retained even with the Bi doping. The EQCM was also used to study the formation and dissolution of Au oxide and preoxide structures formed on the Au substrate electrodes in acidic media. The preoxide structures were AuOH and increased the surface mass. For the formation of stable Au films on quartz wafers, Ti interlayers between Au and quartz was found to be very effective.

  15. Purification, crystallization and preliminary X-ray analysis of OsAREB8 from rice, a member of the AREB/ABF family of bZIP transcription factors, in complex with its cognate DNA

    International Nuclear Information System (INIS)

    Miyazono, Ken-ichi; Koura, Tsubasa; Kubota, Keiko; Yoshida, Takuya; Fujita, Yasunari; Yamaguchi-Shinozaki, Kazuko; Tanokura, Masaru

    2012-01-01

    OsAREB8 from rice (O. sativa), a member of the AREB/ABF family of bZIP transcription factors, was expressed, purified and crystallized using the sitting-drop vapour-diffusion method. A crystal of OsAREB8 in complex with its cognate DNA diffracted X-rays to 3.65 Å resolution. The AREB/ABF family of bZIP transcription factors play a key role in drought stress response and tolerance during the vegetative stage in plants. To reveal the DNA-recognition mechanism of the AREB/ABF family of proteins, the bZIP domain of OsAREB8, an AREB/ABF-family protein from Oryza sativa, was expressed in Escherichia coli, purified and crystallized with its cognate DNA. Crystals of the OsAREB8–DNA complex were obtained by the sitting-drop vapour-diffusion method at 277 K with a reservoir solution consisting of 50 mM MES pH 6.4, 29% MPD, 2 mM spermidine, 20 mM magnesium acetate and 100 mM sodium chloride. A crystal diffracted X-rays to 3.65 Å resolution and belonged to space group C222, with unit-cell parameters a = 155.1, b = 206.7, c = 38.5 Å. The crystal contained one OsAREB8–DNA complex in the asymmetric unit

  16. Crystal structure and DNA-binding property of the ATPase domain of bacterial mismatch repair endonuclease MutL from Aquifex aeolicus.

    Science.gov (United States)

    Fukui, Kenji; Iino, Hitoshi; Baba, Seiki; Kumasaka, Takashi; Kuramitsu, Seiki; Yano, Takato

    2017-09-01

    DNA mismatch repair (MMR) system corrects mismatched bases that are generated mainly by DNA replication errors. The repair system excises the error-containing single-stranded region and enables the re-synthesis of the strand. In the early reactions of MMR, MutL endonuclease incises the newly-synthesized/error-containing strand of the duplex to initiate the downstream excision reaction. MutL endonuclease consists of the N-terminal ATPase and C-terminal endonuclease domains. In this study, we report the crystal structure of the ATPase domain of MutL endonuclease from Aquifex aeolicus. The overall structure of the domain was similar to those of human MutL homologs and Escherichia coli MutL, although E. coli MutL has no endonuclease activity. The ATPase domain was comprised of two subdomains: the N-terminal ATP-binding subdomain and the C-terminal α-β sandwich subdomain. Site-directed mutagenesis experiment identified DNA-interacting eight basic amino acid residues, which were distributed across both the two subdomains and formed a DNA-binding cleft. Docking simulation between the structures of the ATPase and endonuclease domains generated a reliable model structure for the full-length A. aeolicus MutL, which satisfies our previous result of small-angle X-ray scattering analysis. On the basis of the model structure and further experimental results, we concluded that the two separate DNA-binding sites in the full-length A. aeolicus MutL simultaneously bind a dsDNA molecule. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Crystal structure of a Fanconi anemia-associated nuclease homolog bound to 5' flap DNA: basis of interstrand cross-link repair by FAN1

    Energy Technology Data Exchange (ETDEWEB)

    Gwon, Gwang Hyeon; Kim, Youngran; Liu, Yaqi; Watson, Adam T.; Jo, Aera; Etheridge, Thomas J.; Yuan, Fenghua; Zhang, Yanbin; Kim, YoungChang; Carr, Anthony M.; Cho, Yunje

    2014-10-15

    Fanconi anemia (FA) is an autosomal recessive genetic disorder caused by defects in any of 15 FA genes responsible for processing DNA interstrand cross-links (ICLs). The ultimate outcome of the FA pathway is resolution of cross-links, which requires structure-selective nucleases. FA-associated nuclease 1 (FAN1) is believed to be recruited to lesions by a monoubiquitinated FANCI–FANCD2 (ID) complex and participates in ICL repair. Here, we determined the crystal structure of Pseudomonas aeruginosa FAN1 (PaFAN1) lacking the UBZ (ubiquitin-binding zinc) domain in complex with 5' flap DNA. All four domains of the right-hand-shaped PaFAN1 are involved in DNA recognition, with each domain playing a specific role in bending DNA at the nick. The six-helix bundle that binds the junction connects to the catalytic viral replication and repair (VRR) nuclease (VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction. The six-helix bundle also inhibits the cleavage of intact Holliday junctions. PaFAN1 shares several conserved features with other flap structure-selective nucleases despite structural differences. A clamping motion of the domains around the wedge helix, which acts as a pivot, facilitates nucleolytic cleavage. The PaFAN1 structure provides insights into how archaeal Holliday junction resolvases evolved to incise 5' flap substrates and how FAN1 integrates with the FA complex to participate in ICL repair.

  18. Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element.

    Science.gov (United States)

    Narasimhan, Kamesh; Hilbig, Antonia; Udayasuryan, Barath; Jayabal, Sriram; Kolatkar, Prasanna R; Jauch, Ralf

    2014-10-01

    Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6-DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M NH2SO4, 0.1 M MES/imidazole pH 6.5. The data set was indexed and merged in space group C2221, with unit-cell parameters a = 75.74, b = 165.59, c = 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit.

  19. Crystallization and preliminary X-ray diffraction analysis of the Pax9 paired domain bound to a DC5 enhancer DNA element

    Science.gov (United States)

    Narasimhan, Kamesh; Hilbig, Antonia; Udayasuryan, Barath; Jayabal, Sriram; Kolatkar, Prasanna R.; Jauch, Ralf

    2014-01-01

    Pax genes belong to a family of metazoan transcription factors that are known to play a critical role in eye, ear, kidney and neural development. The mammalian Pax family of transcription factors is characterized by a ∼128-amino-acid DNA-binding paired domain that makes sequence-specific contacts with DNA. The diversity in Pax gene activities emerges from complex modes of interaction with enhancer regions and heterodimerization with multiple interaction partners. Based on in vitro optimal binding-site selection studies and enhancer identification assays, it has been suggested that Pax proteins may recognize and bind their target DNA elements with different binding modes/topologies, however this hypothesis has not yet been structurally explored. One of the most extensively studied DNA target elements of the Pax6 paired domain is the eye-lens specific DC5 (δ-crystallin) enhancer element. In order to shed light on Pax6–DC5 DNA interactions, the related paired-domain prototype Pax9 was crystallized with the minimal δ-crystallin DC5 enhancer element and preliminary X-ray diffraction analysis was attempted. A 3.0 Å resolution native data set was collected at the National Synchrotron Light Source (NSLS), Brookhaven from crystals grown in a solution consisting of 10%(w/v) PEG 20K, 20%(v/v) PEG 550 MME, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M NH2SO4, 0.1 M MES/imidazole pH 6.5. The data set was indexed and merged in space group C2221, with unit-cell parameters a = 75.74, b = 165.59, c = 70.14 Å, α = β = γ = 90°. The solvent content in the unit cell is consistent with the presence of one Pax9 paired domain bound to duplex DNA in the asymmetric unit. PMID:25286939

  20. A Low-wear Planar-contact Silicon Raceway for Microball Bearing Applications

    Science.gov (United States)

    2009-04-01

    of friction between stainless steel microballs and silicon grooves (18–20). Both linear and rotary micromotors for sensor platforms were developed...mechanism, like a micromotor , will enable devices to reach higher speeds. Previously, the radial surface wear track depth was >15 m for a device...can lead to significant whirl and axial misalignment, which is critical for micromotor and micropump applications. Small changes in the alignment

  1. Use of the microball for studies of super- and hyper-deformation

    International Nuclear Information System (INIS)

    Sarantites, D.G.

    1995-01-01

    The study of the many fascinating aspects of the highly deformed nuclei at high spin has become possible with multidetector arrays such as Gammasphere that are coming on line. However, the issues of superdeformation in light systems and of hyper-deformation can best be addressed by augmenting Gammasphere with other auxilliary devices such as the Microball. The recent discovery and characterization of a new island of superdeformation in the Z∼38 and N∼44 region, and attempts to observe hyper deformation with Gammasphere in conjunction with the Microball, a 4π charged particle multidetector array, will be reviewed. For light compound systems (A≤120) the Microball enhances considerably the resolving power of Gammasphere using the advantages of 'total spectroscopy' which allows (a) efficient exit channel selection, thus eliminating interfering transitions, (b) dramatic improvement of the energy resolution from event-by-event determination of the recoil direction, which makes possible precise Doppler shift corrections, and (c) selection of cascades originating from high spin states by gating on excitation energy and thus suppressing competing low spin γ cascades. Recent experiments to study the continuum and the discrete line structure of hyper-deformed nuclei (major to minor axis ratio 3:1) will be discussed. These structures appear to be formed only when a proton is emitted among the evaporated particles. Possible scenarios for the role played by this proton will be discussed

  2. Synthesis, spectral, crystal structure, thermal behavior, antimicrobial and DNA cleavage potential of two octahedral cadmium complexes: A supramolecular structure

    Czech Academy of Sciences Publication Activity Database

    Montazerozohori, M.; Musavi, S.A.; Masoudiasl, A.; Naghiha, A.; Dušek, Michal; Kučeráková, Monika

    2015-01-01

    Roč. 137, FEB (2015), s. 389-396 ISSN 1386-1425 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : Schiff base * Cd(II) * DNA cleavage * TG/DTG analysis * X-ray structure analysis Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.653, year: 2015

  3. Miniature quartz crystal-resonator-based thermogravimetric detector.

    Science.gov (United States)

    Sai, N; Tagawa, Y; Sohgawa, M; Abe, T

    2014-09-01

    In this work, a new design for a microheater combined with a quartz crystal microbalance (QCM) array for thermogravimetric analysis is presented. Each QCM consists of two electrodes to excite thickness-shear-mode vibrations and one microheater to increase the temperature on the crystal backside. In addition, all the electrode pads are patterned on the crystal backside, making the design of the QCM compact and user-friendly. Finally, the proposed QCM array was employed to separate ethanol from methanol. This was successfully achieved via thermal desorption spectra calculated by differentiating the frequency changes.

  4. Gold surface supported spherical liposome-gold nano-particle nano-composite for label free DNA sensing.

    Science.gov (United States)

    Bhuvana, M; Narayanan, J Shankara; Dharuman, V; Teng, W; Hahn, J H; Jayakumar, K

    2013-03-15

    Immobilization of 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) liposome-gold nano-particle (DOPE-AuNP) nano-composite covalently on 3-mercaptopropionic acid (MPA) on gold surface is demonstrated for the first time for electrochemical label free DNA sensing. Spherical nature of the DOPE on the MPA monolayer is confirmed by the appearance of sigmoidal voltammetric profile, characteristic behavior of linear diffusion, for the MPA-DOPE in presence of [Fe(CN)(6)](3-/4-) and [Ru(NH(3))(6)](3+) redox probes. The DOPE liposome vesicle fusion is prevented by electroless deposition of AuNP on the hydrophilic amine head groups of the DOPE. Immobilization of single stranded DNA (ssDNA) is made via simple gold-thiol linkage for DNA hybridization sensing in the presence of [Fe(CN)(6)](3-/4-). The sensor discriminates the hybridized (complementary target hybridized), un-hybridized (non-complementary target hybridized) and single base mismatch target hybridized surfaces sensitively and selectively without signal amplification. The lowest target DNA concentration detected is 0.1×10(-12)M. Cyclic voltammetry (CV), electrochemical impedance (EIS), differential pulse voltammetry (DPV) and quartz crystal microbalance (QCM) techniques are used for DNA sensing on DOPE-AuNP nano-composite. Transmission Electron Microscopy (TEM), Fourier Transform Infrared Spectroscopy (FTIR), Atomic Force Microscopy (AFM), Dynamic Light Scattering (DLS) and Ultraviolet-Visible (UV) spectroscopic techniques are used to understand the interactions between the DOPE, AuNP and ssDNA. The results indicate the presence of an intact and well defined spherical DOPE-AuNP nano-composite on the gold surface. The method could be applied for fabrication of the surface based liposome-AuNP-DNA composite for cell transfection studies at reduced reagents and costs. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Synthesis and crystal structure elucidation of new copper(II)-based chemotherapeutic agent coupled with 1,2-DACH and orthovanillin: Validated by in vitro DNA/HSA binding profile and pBR322 cleavage pathway.

    Science.gov (United States)

    Zaki, Mehvash; Afzal, Mohd; Ahmad, Musheer; Tabassum, Sartaj

    2016-08-01

    New copper(II)-based complex (1) was synthesized and characterized by analytical, spectroscopic and single crystal X-ray diffraction. The in vitro binding studies of complex 1 with CT DNA and HSA have been investigated by employing biophysical techniques to examine the binding propensity of 1 towards DNA and HSA. The results showed that 1 avidly binds to CT DNA via electrostatic mode along with the hydrogen bonding interaction of NH2 and CN groups of Schiff base ligand with the base pairs of DNA helix, leads to partial unwinding and destabilization of the DNA double helix. Moreover, the CD spectral studies revealed that complex 1 binds through groove binding interaction that stabilizes the right-handed B-form of DNA. Complex 1 showed an impressive photoinduced nuclease activity generating single-strand breaks in comparison with the DNA cleavage activity in presence of visible light. The mechanistic investigation revealed the efficiency of 1 to cleave DNA strands by involving the generation of reactive oxygen species. Furthermore, the time dependent DNA cleavage activity showed that there was gradual increase in the amount of NC DNA on increasing the photoexposure time. However, the interaction of 1 and HSA showed that the change of intrinsic fluorescence intensity of HSA was induced by the microenvironment of Trp residue. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. A high-performance micro electret power generator based on microball bearings

    International Nuclear Information System (INIS)

    Yang, Zhaohui; Wang, Jing; Zhang, Jinwen

    2011-01-01

    In this paper, a high-performance micro electret power generator fabricated by simple bulk micromachining technology is presented. It has microballs as movable bearings for harvesting changing low-frequency vibration energy from the environment. The silicon V-grooves where the microballs slide have very smooth (1 1 1) planes, and so the device is sensitive to very slight vibration and almost has no resonant frequency. A plasma-enhanced chemical vapour deposition SiO 2 /Si 3 N 4 double layer was used as the electret. The device was fabricated by simple micromachining technology suitable for mass production except for microball assembly. The influence of various frequencies and accelerations on the performance was studied in detail. The measurement results of this electret micro power generator show that the optimal load is proportional to the frequency, and inversely proportional to the acceleration. The peak-to-peak output charge and output power were 72 nC and 5.9 µW respectively at 20 Hz and 0.7 g with the optimal resistive load 626 kΩ. The work frequencies range from 100 Hz to a lower frequency (1 Hz). 112 nW can still be obtained in the minimum acceleration of 0.05 g at 10 Hz with the optimal resistive load, indicating that this device has high sensitivity. The possible application of our device in scavenging energy from low-frequency irregular movements, such as human motion, was proved by a primary experiment

  7. Benzocyclobutene-based electric micromachines supported on microball bearings: Design, fabrication, and characterization

    Science.gov (United States)

    Modafe, Alireza

    This dissertation summarizes the research activities that led to the development of the first microball-bearing-supported linear electrostatic micromotor with benzocyclobutene (BCB) low-k polymer insulating layers. The primary application of this device is long-range, high-speed linear micropositioning. The future generations of this device include rotary electrostatic micromotors and microgenerators. The development of the first generation of microball-bearing-supported micromachines, including device theory, design, and modeling, material characterization, process development, device fabrication, and device test and characterization is presented. The first generation of these devices is based on a 6-phase, bottom-drive, linear, variable-capacitance micromotor (B-LVCM). The design of the electrical and mechanical components of the micromotor, lumped-circuit modeling of the device and electromechanical characteristics, including variable capacitance, force, power, and speed are presented. Electrical characterization of BCB polymers, characterization of BCB chemical mechanical planarization (CMP), development of embedded BCB in silicon (EBiS) process, and integration of device components using microfabrication techniques are also presented. The micromotor consists of a silicon stator, a silicon slider, and four stainless-steel microballs. The aligning force profile of the micromotor was extracted from simulated and measured capacitances of all phases. An average total aligning force of 0.27 mN with a maximum of 0.41 mN, assuming a 100 V peak-to-peak square-wave voltage, was measured. The operation of the micromotor was verified by applying square-wave voltages and characterizing the slider motion. An average slider speed of 7.32 mm/s when excited by a 40 Hz, 120 V square-wave voltage was reached without losing the synchronization. This research has a pivotal impact in the field of power microelectromechanical systems (MEMS). It establishes the foundation for the

  8. Search for hyperdeformation in 146Gd using the microball and gammasphere

    International Nuclear Information System (INIS)

    Hua, P.F.; LaFosse, D.; Korolija, M.; Sarantites, D.G.; Baktash, C.; Cross, C.; Cederwall, B.; Fallon, P.; Lee, I.Y.; Machiavelli, A.

    1994-01-01

    Results from the first attempt to observe hyperdeformation in 146 Gd by the 100 Mo( 51 V, p4n) reaction are presented. The γ-ray spectra were recorded with Gammasphere. The Microball was used to select protons with an efficiency of 90%. A total of 2 x 10 9 proton selected triple events were obtained. The pxn channels comprised ∼25% of the total events. The proton gating decreased the background from competing xn, αxn and fission by a factor of 4

  9. Crystallization and X-ray diffraction analysis of the HMG domain of the chondrogenesis master regulator Sox9 in complex with a ChIP-Seq-identified DNA element

    Energy Technology Data Exchange (ETDEWEB)

    Vivekanandan, Saravanan; Moovarkumudalvan, Balasubramanian; Lescar, Julien; Kolatkar, Prasanna R.

    2015-10-30

    Sox9 is a fundamental sex-determining gene and the master regulator of chondrogenesis, and is involved in the development of various vital organs such as testes, kidney, heart and brain, and in skeletal development. Similar to other known Sox transcription factors, Sox9 recognizes and binds DNA with the consensus sequence C(T/A)TTG(T/A)(T/A) through the highly conserved HMG domain. Nonetheless, the molecular basis of the functional specificity of Sox9 in key developmental processes is still unclear. As an initial step towards a mechanistic understanding of Sox9 transcriptional regulation, the current work describes the details of the purification of the mouse Sox9 HMG domain (mSox9HMG), its crystallization in complex with a ChIP-Seq-identified FOXP2 promoter DNA element and the X-ray diffraction data analysis of this complex. The mSox9HMG–FOXP2 promoter DNA complex was crystallized by the hanging-drop vapour-diffusion method using 20% PEG 3350 in 200 mMsodium/potassium phosphate with 100 mMbis-tris propane at pH 8.5. The crystals diffracted to 2.7 Å resolution and the complex crystallized in the tetragonal space groupP41212, with unit-cell parametersa=b= 99.49,c= 45.89 Å. Crystal-packing parameters revealed that asymmetric unit contained one mSox9HMG–FOXP2 promoter DNA complex with an estimated solvent content of 64%.

  10. A hydrazone Schiff base single crystal (E)-Methyl N"′-(3,4,5-trimethoxybenzylidene) hydrazine carboxylate: Physicochemical, in vitro investigation of antimicrobial activities and molecular docking with DNA gyrase protein

    International Nuclear Information System (INIS)

    Gomathi, G.; Gopalakrishnan, R.

    2016-01-01

    Hydrazone Schiff bases have been widely explored for their antimicrobial, anticancer, anticonvulsant properties. The aim of the present work is to investigate the spectroscopic, electrochemical, thermal properties, in vitro study of antimicrobial activity and molecular docking studies of the MBHC compound. Slow evaporation solution growth technique was used to grow the single crystal of the MBHC compound. Single crystal X-ray diffraction, FTIR and FT-Raman spectroscopic studies are performed and confirmed the grown MBHC compound. UV–Vis spectroscopy and electrochemical studies deduced the absorption region and HOMO-LUMO band gap value of the compound. Resazurin reduction assay method was utilized to perform antibacterial and antifungal studies which resulted in lesser effectiveness of the MBHC compound compared to the erythromycin and fluconazole tablets. Molecular docking of the MBHC compound with the DNA gyrase protein exhibited the good binding affinity with energy of − 43.196 kcal/mol and docking score of − 6.266 and having good interaction with aminoacids – ASP81 and ARG84. - Highlights: • MBHC single crystal was grown by employing slow evaporation solution growth technique. • The compound crystallizes in monoclinic crystal system with space group P2_1/c. • The HOMO-LUMO band gap value was found to be 1.96 eV. • The compound has lesser antimicrobial activity when compared to erythromycin and fluconazole. • MBHC shows better binding affinity towards DNA gyrase protein.

  11. A hydrazone Schiff base single crystal (E)-Methyl N{sup ′}-(3,4,5-trimethoxybenzylidene) hydrazine carboxylate: Physicochemical, in vitro investigation of antimicrobial activities and molecular docking with DNA gyrase protein

    Energy Technology Data Exchange (ETDEWEB)

    Gomathi, G.; Gopalakrishnan, R., E-mail: krgkrishnan@annauniv.edu

    2016-07-01

    Hydrazone Schiff bases have been widely explored for their antimicrobial, anticancer, anticonvulsant properties. The aim of the present work is to investigate the spectroscopic, electrochemical, thermal properties, in vitro study of antimicrobial activity and molecular docking studies of the MBHC compound. Slow evaporation solution growth technique was used to grow the single crystal of the MBHC compound. Single crystal X-ray diffraction, FTIR and FT-Raman spectroscopic studies are performed and confirmed the grown MBHC compound. UV–Vis spectroscopy and electrochemical studies deduced the absorption region and HOMO-LUMO band gap value of the compound. Resazurin reduction assay method was utilized to perform antibacterial and antifungal studies which resulted in lesser effectiveness of the MBHC compound compared to the erythromycin and fluconazole tablets. Molecular docking of the MBHC compound with the DNA gyrase protein exhibited the good binding affinity with energy of − 43.196 kcal/mol and docking score of − 6.266 and having good interaction with aminoacids – ASP81 and ARG84. - Highlights: • MBHC single crystal was grown by employing slow evaporation solution growth technique. • The compound crystallizes in monoclinic crystal system with space group P2{sub 1}/c. • The HOMO-LUMO band gap value was found to be 1.96 eV. • The compound has lesser antimicrobial activity when compared to erythromycin and fluconazole. • MBHC shows better binding affinity towards DNA gyrase protein.

  12. Rhenium complexes of chromophore-appended dipicolylamine ligands: syntheses, spectroscopic properties, DNA binding and X-ray crystal structure

    International Nuclear Information System (INIS)

    Mullice, L.A.; Buurma, N.J.; Pope, S.J.A.; Laye, R.H.; Harding, L.P.

    2008-01-01

    The syntheses of two chromophore-appended dipicolylamine-derived ligands and their reactivity with penta-carbonyl-chloro-rhenium have been studied. The resultant complexes each possess the fac-Re(CO) 3 core. The ligands L 1 1-[bis(pyridine-2-yl-methyl)amino]methyl-pyrene and L 2 2-[bis(pyridine-2-yl-methyl)amino]methyl-quinoxaline were isolated via a one-pot reductive amination in moderate yield. The corresponding rhenium complexes were isolated in good yields and characterised by 1 H NMR, MS, IR and UV-Vis studies. X-Ray crystallographic data were obtained for fac-{Re(CO) 3 (L 1 )}(BF 4 ), C 34 H 26 BF 4 N 4 O 3 Re: monoclinic, P2(1)/c, a 18.327(2) Angstroms, α = 90.00 degrees, b 14.1537(14) Angstroms, β96.263(6) degrees, c = 23.511(3) Angstroms, γ 90.00 Angstroms, 6062.4(11) (Angstroms) 3 , Z=8. The luminescence properties of the ligands and complexes were also investigated, with the emission attributed to the appended chromophore in each case. Isothermal titration calorimetry suggests that fac-{Re(CO) 3 (L 1 )}(BF 4 ) self-aggregates cooperatively in aqueous solution, probably forming micelle-like aggregates with a cmc of 0.18 mM. Investigations into the DNA-binding properties of fac-{Re(CO) 3 (L 1 )}(BF 4 ) were undertaken and revealed that fac-{Re(CO) 3 (L 1 )}(BF 4 ) binding to fish sperm DNA (binding constant 1.5 ± 0.2 * 10 5 M -1 , binding site size 3.2 ± 0.3 base pairs) is accompanied by changes in the UV-Vis spectrum as typically observed for pyrene-based intercalators while the calorimetrically determined binding enthalpy (-14 ± 2 kcal mol -1 ) also agrees favourably with values as typically found for intercalators. (authors)

  13. Amine free crystal structure: The crystal structure of d(CGCGCG)2 and methylamine complex crystal

    International Nuclear Information System (INIS)

    Ohishi, Hirofumi; Tsukamoto, Koji; Hiyama, Yoichi; Maezaki, Naoyoshi; Tanaka, Tetsuaki; Ishida, Toshimasa

    2006-01-01

    We succeeded in the crystallization of d(CGCGCG) 2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2F o - F c map was much clear and easily traced. It is First time monoamine co-crystallizes with d(CGCGCG) 2 . However, methylamine was not found from the complex crystal of d(CGCGCG) 2 and methylamine. Five Mg ions were found around d(CGCGCG) 2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg 2+ . DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG) 2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this

  14. Cyto-genotoxic and DNA methylation changes induced by different crystal phases of TiO{sub 2}-np in bronchial epithelial (16-HBE) cells

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, Manosij, E-mail: gmanosij@gmail.com [K.U.Leuven, Department of Public Health and Primary Care, Centre Environment & Health, B-3000 Leuven (Belgium); Öner, Deniz; Duca, Radu-Corneliu [K.U.Leuven, Department of Public Health and Primary Care, Centre Environment & Health, B-3000 Leuven (Belgium); Cokic, Stevan M. [Department of Oral Health Sciences, KU Leuven BIOMAT, 3000 Leuven (Belgium); Seys, Sven [K.U.Leuven, Department of Immunology and Microbiology, Leuven (Belgium); Kerkhofs, Stef [Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200f, Heverlee, Leuven (Belgium); Van Landuyt, Kirsten [Department of Oral Health Sciences, KU Leuven BIOMAT, 3000 Leuven (Belgium); Hoet, Peter [K.U.Leuven, Department of Public Health and Primary Care, Centre Environment & Health, B-3000 Leuven (Belgium); Godderis, Lode, E-mail: lode.godderis@med.kuleuven.be [K.U.Leuven, Department of Public Health and Primary Care, Centre Environment & Health, B-3000 Leuven (Belgium); Idewe, External Service for Prevention and Protection at Work, B-3001, Heverlee (Belgium)

    2017-02-15

    Highlights: • Comet and micronucleus (with and without CytB) assays revealed significant genotoxic effect of TiO{sub 2}-np. • TiO{sub 2}-np induces cell cycle arrest in the S-phase. • Anatase form induces more cyto-genotoxic effect compared to rutile and anatase-rutile mixture. • Significant hypomethylation were observed at for anatase, rutile and anatase: rutile mixture. - Abstract: With the increase in use of TiO{sub 2}-np, a better understanding of their safety is important. In the present study the effect of different crystal phases of TiO{sub 2}-np (anatase, rutile and anatase: rutile mixture; 20–26 nm) were studied for cyto-genotoxicity and global DNA methylation and hydroxymethylation. Cytotoxic response was observed at a concentration of 25 μg/ml for the particles tested. Results of comet and micronucleus (with and without CytB) assays revealed significant genotoxic effect of these particles. Flow cytometry revealed cell cycle arrest in the S-phase. Based on the results, toxicity of the particles could be correlated with their physico-chemical properties (i.e. smaller size and hydrodynamic diameter and larger surface area), anatase form being the most toxic. From the results of the cyto-genotoxicity assays, concentrations were determined for the epigenetic study. Effect on global DNA methylation and hydroxymethylation levels were studied at cyto-genotoxic (25 μg/ml), genotoxic (12.5 μg/ml) and sub cyto-genotoxic (3.25 μg/ml) concentrations using LC–MS/MS analysis. Though no significant changes were observed for 3 h treatment schedule; significant hypomethylation were observed at 24 h for anatase (significant at 3.25 and 25 μg/ml), rutile (significant at 3.25 and 25 μg/ml) and anatase: rutile mixture (significant at 25 μg/ml) forms. The results suggest that epigenetic changes could occur at sub cyto-genotoxic concentrations. And hence for complete characterization of nanoparticle toxicity, epigenetic studies should be performed along with

  15. Development of A Microbalance System For Water and Dust Detection In Mars

    Science.gov (United States)

    Battaglia, R.; Palomba, E.; Palumbo, P.; Colangeli, L.

    .e. the caps, the regolith and the ice hazes. Ice hazes, in fact, provide a mechanism for scavenging water vapor in the thin Mars atmosphere and may play a key role in the seasonal cycle of water on Mars. A focused investigation, made in different regions, possibly in different seasons, and spanning several days is desirable for solving the question of linkage of water cycle with these sources. The objective of our research program is the development and pro- duction of a microbalance measurement system . It will be able to measure in situ, for the first time, directly and quantitatively, the cumulative dust mass flux and the water vapour abundance in a Martian environment. A preliminary study of this process at Mars average conditions showed that available microbalances can detect water ice condensed on their surface in few seconds, after dew or frost point is reached and similar evaluations have been made with respect to expected dust deposition rate on Mars surface, based on data from MAE experiment onboard the Sojourner rover. The measuring system will be devoted to study the dynamic of the Martian water and dust cycles. In detail, our goals are: - Study of the Martian water and dust cycles (seasonal, diurnal) and their links; - Investigation of the brines formation and evaporation mech- anisms and their interaction with the regolith; - Investigation of mechanism of diurnal water release by the regolith and its weight as water atmospheric reservoir; - Study of the dust settling rates and their possible correlation with environmental conditions at the landing sites (temperature, pressure, winds); - Study of the local dust storm and devils raising mechanisms; - Investigation of the main modes of aeolian transport of grains and dust raising. We discuss the use of microbalances for the scientific applica- tions to Martian environment studies

  16. Electrografting of carboxyphenyl thin layer onto gold for DNA and enzyme immobilization

    International Nuclear Information System (INIS)

    Nowicka, Anna M.; Fau, Michal; Kowalczyk, Agata; Strawski, Marcin; Stojek, Zbigniew

    2014-01-01

    The convenient functionalization of metal surfaces by carboxyphenyl groups in aprotic media is not possible for two reasons. First, carboxy derivatives of diazonium salts are very unstable and, second, the electroreduction product is soluble in the solvent. So, the optimization of the conditions of the electrografting of the metal surfaces by applying aqueous solutions is much needed. Compared to earlier cyclic voltammetry approaches we have shown that the chronoamperometric deposition is more convenient. The constant potential equal to the voltammetric peak potential and the molar ratio 1:1 for the substrates: 4-aminobenzoic acid and NaNO 2 as the diazotization agent, in 0.5 M HCl, appeared to be very satisfying conditions for the deposition of a thin layer of deposit of perpendicularly oriented carboxyphenyl groups at the Au surface and for maximal elimination of the influence of the side-reactions products. Under the determined conditions the immobilization of DNA strands was optimal and the deposited laccase layer was tightly packed and very efficient toward the electroreduction of oxygen. Electrochemical impedance spectroscopy, electrochemical quartz crystal microbalance, cyclic voltammetry, chronocoulometry, atomic force microscopy, contact angle measurements and UV–Vis spectroscopy of the solution were used to characterize the electrografted carboxyphenyl layers and subsequent oligonucleotide and enzyme immobilization process

  17. Blueprint of quartz crystal microbalance biosensor for early detection of breast cancer through salivary autoantibodies against ATP6AP1.

    Science.gov (United States)

    Arif, Sania; Qudsia, Syeda; Urooj, Samina; Chaudry, Nazia; Arshad, Aneeqa; Andleeb, Saadia

    2015-03-15

    Breast cancer represents a significant health problem because of its high prevalence. Tests like mammography, which are used abundantly for the detection of breast cancer, suffer from serious limitations. Mammography correctly detects malignancy about 80-90% of the times, failing in places when (1) the tumor is small at early stage, (2) breast tissue is dense or (3) in women of less than 40 years. Serum-based detection of biomarkers involves risk of disease transfer, along with other concerns. These techniques compromise in the early detection of breast cancer. Early detection of breast cancer is a crucial factor to enhance the survival rate of patient. Development of regular screening tests for early diagnosis of breast cancer is a challenge. This review highlights the design of a handy and household biosensor device aimed for self-screening and early diagnosis of breast cancer. The design makes use of salivary autoantibodies for specificity to develop a noninvasive procedure, breast cancer specific biomarkers for precision for the development of device, and biosensor technology for sensitivity to screen the early cases of breast cancer more efficiently. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Crystal structure, DNA binding, cleavage, antioxidant and antibacterial studies of Cu(II), Ni(II) and Co(III) complexes with 2-((furan-2-yl)methylimino)methyl)-6-ethoxyphenol Schiff base

    Science.gov (United States)

    Venkateswarlu, Kadtala; Kumar, Marri Pradeep; Rambabu, Aveli; Vamsikrishna, Narendrula; Daravath, Sreenu; Rangan, Krishnan; Shivaraj

    2018-05-01

    Three novel binary metal complexes; 1 [Cu(L)2], 2 [Ni(L)2] and 3 [Co(L)3] where, L (2-(((furan-2-yl) methylimino)methyl)-6-ethoxyphenol, C14H15NO3), were synthesized and characterized by various spectral techniques. Based on spectral studies square planar geometry is assigned for Cu(II) and Ni(II) complexes, whereas Co(III) owned octahedral geometry. Ligand, [Cu(L)2] and [Ni(L)2] are crystallized and found to be monoclinic crystal systems. CT-DNA absorption binding studies revealed that the complexes show good binding propensity (Kb = 5.02 × 103 M-1, 2.77 × 103 M-1, 1.63 × 104 M-1 for 1, 2 and 3 respectively). The role of these complexes in the oxidative and photolytic cleavage of supercoiled pBR322 DNA was studied and found that the complexes cleave the pBR322 DNA effectively. The catalytic ability of 1, 2 and 3 follows the order: 3 > 1 >2. Antioxidant studies of the new complexes revealed that they exhibit significant antioxidant activity against DPPH radical. The Schiff base and its metal complexes have been screened for antibacterial studies by Minimum Inhibitory Concentration method. It is observed that all metal complexes showed more activity than free ligand.

  19. Thermal decomposition of hydrotalcite-like compounds studied by a novel tapered element oscillating microbalance (TEOM)

    International Nuclear Information System (INIS)

    Perez-Ramirez, Javier; Abello, Sonia

    2006-01-01

    For the first time, we report on the application of a tapered element oscillating microbalance (TEOM) as a novel technique to investigate the thermal decomposition of hydrotalcite-like compounds (HTlcs) in air. Experiments were performed in the temperature range of 323-973 K with Mg-Al, Ni-Al, and Co-Al-HTlcs. The TEOM technique measures mass changes based on inertial forces, presenting important advantages over conventional thermogravimetric analyzers, such as the very rapid time response and the well-defined flow pattern. In general terms, excellent agreement between TEOM, TGA, and DTA techniques during HTlc decomposition was obtained. Interestingly, transition temperatures in the TEOM were lower than in TGA and DTA, particularly for removal of interlayer water but also for dehydroxylation of the brucite-like layers and decarbonation. This was attributed to the flow-through operation in the tapered element of the TEOM as compared to the recognized gas stagnancy and bypass in sample crucibles of conventional thermogravimetric analyzers. Our results conclude that the TEOM technique is suitable for temperature-programmed studies. However, due to its operation principle, blank runs are required in contrast to the more automatic operation in commercial thermogravimetric units. Besides, a careful sample loading and packing in the micro-reactor is essential for reproducible results

  20. Racemic DNA crystallography.

    Science.gov (United States)

    Mandal, Pradeep K; Collie, Gavin W; Kauffmann, Brice; Huc, Ivan

    2014-12-22

    Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L- and D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four-way junction, showing that the advantages of racemic crystallography should extend to DNA. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Synthesis and crystal structure determination of copper(II)-complex: In vitro DNA and HSA binding, pBR322 plasmid cleavage, cell imaging and cytotoxic studies.

    Science.gov (United States)

    Tabassum, Sartaj; Zaki, Mehvash; Ahmad, Musheer; Afzal, Mohd; Srivastav, Saurabh; Srikrishna, Saripella; Arjmand, Farukh

    2014-08-18

    New Cu(II) complex 1 of indole-3-propionic acid and 1,10-phenanthroline was synthesized and characterized by analytical, spectroscopic and single crystal X-ray diffraction. In vitro DNA binding studies of 1 was performed by employing UV-vis and fluorescence spectroscopic techniques. The binding affinity towards human serum albumin (HSA) was also investigated to understand the carrier role in body system, as the time dependent HPLC experiment of 1 revealed that bonded drug with protein releases slowly in presence of DNA. Complex 1 exhibited good anti-tumor activity (GI50 values <10 μg/ml), and to elucidate the mechanism of tumor inhibition, topoisomerase I enzymatic activity was carried out and further validated by cell imaging studies which clearly showed its nuclear localization. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  2. The sublimation kinetics of GeSe single crystals

    Science.gov (United States)

    Irene, E. A.; Wiedemeier, H.

    1975-01-01

    The sublimation kinetics of (001) oriented GeSe single crystal platelets was studied by high-temperature mass spectroscopy, quantitative vacuum microbalance techniques, and hot stage optical microscopy. For a mean experimental temperature of 563 K, the activation enthalpy and entropy are found to equal 32.3 kcal/mole and 19.1 eu, respectively. The vaporization coefficient is less than unity for the range of test temperatures, and decreases with increasing temperature. The combined experimental data are correlated by means of a multistep surface adsorption mechanism.

  3. Application of the TEOM reactor for adsorption, diffusion and kinetic studies[TEOM=Tapered Element Oscillating Microbalance

    Energy Technology Data Exchange (ETDEWEB)

    Rebo, Hans Petter

    1999-07-01

    In Norway, the limited offshore oil resources, the abundance of natural gas and the need to recover associated gas from the crude oil production have made the utilisation of natural gas the focus of increased attention. Most products from refineries and chemical industry are formed by gas phase reactions over solid materials like metals, metal oxides and zeolites. Heterogeneous catalysts are in addition frequently used for environmental purposes and energy production. In the work described in this thesis, an experimental set-up was built and used to study some typical processes in heterogeneous catalysis. The set-up included a tapered element oscillating microbalance (TEOM) for measuring mass changes. The following properties of the TEOM were found particularly useful: (1) Frequent frequency counting makes the TEOM suitable for recording transient uptake curves, (2) High sensitivity of the microbalance makes it possible to work with low catalyst loading and still obtain high signal to noise ratio, and (3) Reliable kinetic data are obtained due to the fixed bed characteristics of the TEOM. Adsorption and diffusion of o-xylene and toluene in a commercial HZSM-5 zeolite were studied at 30, 100 and 200 {sup o}C and at partial pressures in the range of 0.002-0.1 bar. The effect of coke on the adsorption and diffusion properties were studied by adsorption experiments at 30 {sup o}C of ethane, toluene and n-hexane before and after coke formation during ethene oligomerisation at 475 {sup o}C and at P(ethene)=0.8 bar. The oligomerisation of ethene over HZSM-5 was used as a model reaction for comparing coke formation in a gravimetric microbalance and in the TEOM. The work also includes a study of coke formation and the effect of coke on the kinetics of propene dehydrogenation over Pt-Sn/Al{sub 2}O{sub 3} catalysts at 500-580 {sup o}C.

  4. Crystal structures of palladium(II) ternary complexes of 5-x-2-aminobenzoic acid with 1,10-phenanthroline and their interaction with calf thymus DNA (where X=Cl, Br and I).

    Science.gov (United States)

    Wang, Yue; Okabe, Nobuo; Odoko, Mamiko

    2005-10-01

    The crystal structures of a series of three palladium(II) ternary complexes of 5-halogeno-2-aminobenzoic acid (5-X-AB, where X=Cl, Br and I) with 1,10-phenanthroline [Pd(5-Cl-AB)(phen)] (1), [Pd(5-Br-AB)(phen)] (2) and [Pd(5-I-AB)(phen)] (3) have been determined, and their coordination geometries and the crystal architecture characterized. All of the complexes are an isostructure in which each Pd(II) atom has basically similar square planar coordination geometry. The substitute halogen group at 5-position of AB plays an important role in producing the coordination bonds of the carboxylate and amino groups in which the carboxylate O atom and the amino N atom act as the negative monodentate ligand atoms. The coordination bond distances of O-Pd increase in the order 1<2<3, while those of N-Pd decrease in the same order. The binding of the complexes to the calf thymus DNA has also been studied by the fluorescence method. Each of the complexes shows high binding propensity to DNA which can be reflected as the relative order 1<2<3.

  5. X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition: N-Terminal Region of M-MuLV Integrase

    Energy Technology Data Exchange (ETDEWEB)

    Guan, Rongjin [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Aiyer, Sriram [Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Cote, Marie L. [Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway New Jersey 08854; Xiao, Rong [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Jiang, Mei [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Acton, Thomas B. [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Roth, Monica J. [Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Montelione, Gaetano T. [Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway New Jersey 08854; Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway New Jersey 08854

    2017-02-03

    The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain, and the C-terminal domain. The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1–44) and an HHCC zinc-finger NTD (residues 45–105), in two crystal forms are reported. The structures of IN NTR constructs encoding residues 1–105 (NTR1–105) and 8–105 (NTR8–105) were determined at 2.7 and 2.15 Å resolution, respectively and belong to different space groups. While both crystal forms have similar protomer structures, NTR1–105 packs as a dimer and NTR8–105 packs as a tetramer in the asymmetric unit. The structure of the NED consists of three anti-parallel β-strands and an α-helix, similar to the NED of prototype foamy virus (PFV) IN. These three β-strands form an extended β-sheet with another β-strand in the HHCC Zn2+ binding domain, which is a unique structural feature for the M-MuLV IN. The HHCC Zn2+ binding domain structure is similar to that in HIV and PFV INs, with variations within the loop regions. Differences between the PFV and MLV IN NEDs localize at regions identified to interact with the PFV LTR and are compared with established biochemical and virological data for M-MuLV. Proteins 2017; 85:647–656.

  6. Boron-Doped Carbon Nano-/Microballs from Orthoboric Acid-Starch: Preparation, Characterization, and Lithium Ion Storage Properties

    Directory of Open Access Journals (Sweden)

    Xinhua Lu

    2018-01-01

    Full Text Available A boron-doped carbon nano-/microballs (BC was successfully obtained via a two-step procedure including hydrothermal reaction (180°C and carbonization (800°C with cheap starch and H3BO3 as the carbon and boron source. As a new kind of boron-doped carbon, BC contained 2.03 at% B-content and presented the morphology as almost perfect nano-/microballs with different sizes ranging from 500 nm to 5 μm. Besides that, due to the electron deficient boron, BC was explored as anode material and presented good lithium storage performance. At a current density of 0.2 C, the first reversible specific discharge capacity of BC electrode reached as high as 964.2 mAh g–1 and kept at 699 mAh g–1 till the 11th cycle. BC also exhibited good cycle ability with a specific capacity of 356 mAh g–1 after 79 cycles at a current density of 0.5 C. This work proved to be an effective approach for boron-doped carbon nanostructures which has potential usage for lithium storage material.

  7. Crystal structure of clustered regularly interspaced short palindromic repeats (CRISPR)-associated Csn2 protein revealed Ca2+-dependent double-stranded DNA binding activity.

    Science.gov (United States)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong

    2011-09-02

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.

  8. Crystal Structure of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Csn2 Protein Revealed Ca[superscript 2+]-dependent Double-stranded DNA Binding Activity

    Energy Technology Data Exchange (ETDEWEB)

    Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)

    2012-05-22

    Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.

  9. Whole-bacterium SELEX of DNA aptamers for rapid detection of E.coli O157:H7 using a QCM sensor.

    Science.gov (United States)

    Yu, Xiaofan; Chen, Fang; Wang, Ronghui; Li, Yanbin

    2018-01-20

    The rapid detection of foodborne pathogens is critical to ensure food safety. The objective of this study is to select aptamers specifically bound to Escherichia coli O157:H7 using the whole-bacterium SELEX (Systematic Evolution of Ligands by Exponential Enrichment) and apply the selected aptamer to a QCM (quartz crystal microbalance) sensor for rapid and sensitive detection of target bacteria. A total of 19 rounds of selection against live E. coli O157:H7 and 6 rounds of counter selection against a mixture of Staphylococcus aureus, Listeria monocytogenes, and Salmonella Typhimurium, were performed. The aptamer pool from the last round was cloned and sequenced. One sequence S1 that appeared 16 times was characterized and a dissociation constant (K d ) of 10.30nM was obtained. Subsequently, a QCM aptasensor was developed for the rapid detection of E. coli O157:H7. The limit of detection (LOD) and the detection time of the aptasensor was determined to be 1.46×10 3 CFU/ml and 50min, respectively. This study demonstrated that the ssDNA aptamer selected by the whole-bacterium SELEX possessed higher sensitivity than previous work and the potential use of the constructed QCM aptasensor in rapid screening of foodborne pathogens. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  11. Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda).

    Science.gov (United States)

    Seng, Hoi-Ling; Ong, Han-Kiat Alan; Rahman, Raja Noor Zaliha Raja Abd; Yamin, Bohari M; Tiekink, Edward R T; Tan, Kong Wai; Maah, Mohd Jamil; Caracelli, Ignez; Ng, Chew Hee

    2008-11-01

    The binding selectivity of the M(phen)(edda) (M=Cu, Co, Ni, Zn; phen=1,10-phenanthroline, edda=ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(II) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N(4)O(2) octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling.

  12. Racemic DNA Crystallography

    OpenAIRE

    Mandal , Pradeep K.; Collie , Gavin W.; Kauffmann , Brice; Huc , Ivan

    2014-01-01

    International audience; Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic-protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of Land D-deoxyribo-oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propens...

  13. The discovery of X-rays diffraction: From crystals to DNA. A case study to promote understanding of the nature of science and of its interdisciplinary character

    International Nuclear Information System (INIS)

    Guerra, Francesco; Leone, Matteo; Robotti, Nadia

    2015-01-01

    The advantages of introducing history of science topics into the teaching of science has been advocated by a large number of scholars within the science education community. One of the main reasons given for using history of science in teaching is its power to promote understanding of the nature of science (NOS). In this respect, the historical case of X-rays diffraction, from the discovery of Max von Laue (1912) to the first X-rays diffraction photographs of DNA (1953), is a case in point for showing that a correct experimental strategy and a favourable theoretical context are not enough to make a scientific discovery.

  14. Crystals in crystals

    DEFF Research Database (Denmark)

    Christensen, Claus H.; Schmidt, I.; Carlsson, A.

    2005-01-01

    A major factor governing the performance of catalytically active particles supported on a zeolite carrier is the degree of dispersion. It is shown that the introduction of noncrystallographic mesopores into zeolite single crystals (silicalite-1, ZSM-5) may increase the degree of particle dispersion....... As representative examples, a metal (Pt), an alloy (PtSn), and a metal carbide (beta-Mo2C) were supported on conventional and mesoporous zeolite carriers, respectively, and the degree of particle dispersion was compared by TEM imaging. On conventional zeolites, the supported material aggregated on the outer surface...

  15. Virtual Crystallizer

    Energy Technology Data Exchange (ETDEWEB)

    Land, T A; Dylla-Spears, R; Thorsness, C B

    2006-08-29

    Large dihydrogen phosphate (KDP) crystals are grown in large crystallizers to provide raw material for the manufacture of optical components for large laser systems. It is a challenge to grow crystal with sufficient mass and geometric properties to allow large optical plates to be cut from them. In addition, KDP has long been the canonical solution crystal for study of growth processes. To assist in the production of the crystals and the understanding of crystal growth phenomena, analysis of growth habits of large KDP crystals has been studied, small scale kinetic experiments have been performed, mass transfer rates in model systems have been measured, and computational-fluid-mechanics tools have been used to develop an engineering model of the crystal growth process. The model has been tested by looking at its ability to simulate the growth of nine KDP boules that all weighed more than 200 kg.

  16. single crystals

    Indian Academy of Sciences (India)

    2018-05-18

    May 18, 2018 ... Abstract. 4-Nitrobenzoic acid (4-NBA) single crystals were studied for their linear and nonlinear optical ... studies on the proper growth, linear and nonlinear optical ..... between the optic axes and optic sign of the biaxial crystal.

  17. Crystal Systems.

    Science.gov (United States)

    Schomaker, Verner; Lingafelter, E. C.

    1985-01-01

    Discusses characteristics of crystal systems, comparing (in table format) crystal systems with lattice types, number of restrictions, nature of the restrictions, and other lattices that can accidently show the same metrical symmetry. (JN)

  18. Monomial Crystals and Partition Crystals

    Science.gov (United States)

    Tingley, Peter

    2010-04-01

    Recently Fayers introduced a large family of combinatorial realizations of the fundamental crystal B(Λ0) for ^sln, where the vertices are indexed by certain partitions. He showed that special cases of this construction agree with the Misra-Miwa realization and with Berg's ladder crystal. Here we show that another special case is naturally isomorphic to a realization using Nakajima's monomial crystal.

  19. Crystal structure of MboIIA methyltransferase

    OpenAIRE

    Osipiuk, Jerzy; Walsh, Martin A.; Joachimiak, Andrzej

    2003-01-01

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-l-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 Å resolution the crystal structure of a β-class DNA MTase MboIIA (M·MboIIA) from the bacterium Moraxella bovis,...

  20. DNA-guided nanoparticle assemblies

    Science.gov (United States)

    Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel

    2013-07-16

    In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.

  1. Study of the electrodeposition of rhenium thin films by electrochemical quartz microbalance and X-ray photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Schrebler, R.; Cury, P.; Suarez, C.; Munoz, E.; Vera, F.; Cordova, R.; Gomez, H.; Ramos-Barrado, J.R.; Leinen, D.; Dalchiele, E.A.

    2005-01-01

    Rhenium thin films were prepared by electrodeposition from an aqueous solution containing 0.1 M Na 2 SO 4 +H 2 SO 4 , pH 2 in presence of y mM HReO 4 . As substrates polycrystalline gold (y=0.75 mM HReO 4 ) and monocrystalline n-Si(100) (y=40 mM HReO 4 ) were used. The electrochemical growth of rhenium was studied by cyclic voltammetry and electrochemical quartz microbalance on gold electrodes. The results found in the potential region before the hydrogen evolution reaction (her) showed that ReO 3 , ReO 2 and Re 2 O 3 with different hydration grades can be formed. In the potential region where the her is occurring, either on gold or n-Si(100) the electrodeposition of metallic rhenium takes place. On both substrates, rhenium films were formed by electrolysis at constant potential and X-ray photoelectron spectroscopy technique was used to characterise these deposits. It was concluded that the electrodeposited films were of metallic rhenium and only the uppermost atomic layer contained rhenium oxide species

  2. Crystallization mechanisms of acicular crystals

    Science.gov (United States)

    Puel, François; Verdurand, Elodie; Taulelle, Pascal; Bebon, Christine; Colson, Didier; Klein, Jean-Paul; Veesler, Stéphane

    2008-01-01

    In this contribution, we present an experimental investigation of the growth of four different organic molecules produced at industrial scale with a view to understand the crystallization mechanism of acicular or needle-like crystals. For all organic crystals studied in this article, layer-by-layer growth of the lateral faces is very slow and clear, as soon as the supersaturation is high enough, there is competition between growth and surface-activated secondary nucleation. This gives rise to pseudo-twinned crystals composed of several needle individuals aligned along a crystallographic axis; this is explained by regular over- and inter-growths as in the case of twinning. And when supersaturation is even higher, nucleation is fast and random. In an industrial continuous crystallization, the rapid growth of needle-like crystals is to be avoided as it leads to fragile crystals or needles, which can be partly broken or totally detached from the parent crystals especially along structural anisotropic axis corresponding to weaker chemical bonds, thus leading to slower growing faces. When an activated mechanism is involved such as a secondary surface nucleation, it is no longer possible to obtain a steady state. Therefore, the crystal number, size and habit vary significantly with time, leading to troubles in the downstream processing operations and to modifications of the final solid-specific properties. These results provide valuable information on the unique crystallization mechanisms of acicular crystals, and show that it is important to know these threshold and critical values when running a crystallizer in order to obtain easy-to-handle crystals.

  3. In-situ quartz crystal microgravimetric studies of molecular adsorbates containing thiol and hydroquinone moieties bound to Au(111) surfaces in aqueous electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Y.; Sukenik, C.; Sandifer, M. [Case Western Univ., Cleveland, OH (United States); Barriga, R.J.; Soriaga, M.P.; Scherson, D. [Texas A& M Univ., College Station, TX (United States)

    1995-12-01

    The microgravimetric properties of monolayers of 2, 5-dihydroxythiophenol, 2,5-dihydroxybenzyl mercaptan, and 2, 5-dihydroxy-4-methylbenzyl mercaptan adsorbed on Au(111) single crystal electrodes were examined by in situ quartz crystal microbalance techniques in aqueous perchloric acid electrolytes. The results obtained are consistent with the reversible loss of an average of about three waters per adsorbed molecule as the layers are oxidized and subsequently reduced. These observations provide evidence for discrete changes in the extent of bound water within the hydroquinone/quinone layer as the oxidation state of the monolayer is changed. 9 refs., 4 figs.

  4. Effect of temperature on DNA double helix: An insight from ...

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... We have carried out detailed MD simulations of DNA double ..... Wireframe representation of B-DNA crystal structures with PDB identifier (a) 1EHV, ..... nucleic acid structures, PhD thesis, University of Calcutta, Kolkata.

  5. A signal amplification assay for HSV type 1 viral DNA detection using nanoparticles and direct acoustic profiling

    Directory of Open Access Journals (Sweden)

    Hammond Richard

    2010-02-01

    Full Text Available Abstract Background Nucleic acid based recognition of viral sequences can be used together with label-free biosensors to provide rapid, accurate confirmation of viral infection. To enhance detection sensitivity, gold nanoparticles can be employed with mass-sensitive acoustic biosensors (such as a quartz crystal microbalance by either hybridising nanoparticle-oligonucleotide conjugates to complimentary surface-immobilised ssDNA probes on the sensor, or by using biotin-tagged target oligonucleotides bound to avidin-modified nanoparticles on the sensor. We have evaluated and refined these signal amplification assays for the detection from specific DNA sequences of Herpes Simplex Virus (HSV type 1 and defined detection limits with a 16.5 MHz fundamental frequency thickness shear mode acoustic biosensor. Results In the study the performance of semi-homogeneous and homogeneous assay formats (suited to rapid, single step tests were evaluated utilising different diameter gold nanoparticles at varying DNA concentrations. Mathematical models were built to understand the effects of mass transport in the flow cell, the binding kinetics of targets to nanoparticles in solution, the packing geometries of targets on the nanoparticle, the packing of nanoparticles on the sensor surface and the effect of surface shear stiffness on the response of the acoustic sensor. This lead to the selection of optimised 15 nm nanoparticles that could be used with a 6 minute total assay time to achieve a limit of detection sensitivity of 5.2 × 10-12 M. Larger diameter nanoparticles gave poorer limits of detection than smaller particles. The limit of detection was three orders of magnitude lower than that observed using a hybridisation assay without nanoparticle signal amplification. Conclusions An analytical model was developed to determine optimal nanoparticle diameter, concentration and probe density, which allowed efficient and rapid optimisation of assay parameters

  6. Interaction of Soybean 7S Globulin Peptide with Cell Membrane Model via Isothermal Titration Calorimetry, Quartz Crystal Microbalance with Dissipation, and Langmuir Monolayer Study.

    Science.gov (United States)

    Zou, Yuan; Pan, Runting; Ruan, Qijun; Wan, Zhili; Guo, Jian; Yang, Xiaoquan

    2018-05-16

    To understand the underlying molecular mechanism of the cholesterol-lowering effect of soybean 7S globulins, the interactions of their pepsin-released peptides (7S-peptides) with cell membrane models consisting of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), and cholesterol (CHOL) were systematically studied. The results showed that 7S-peptides were bound to DPPC/DOPC/CHOL liposomes mainly through van der Waals forces and hydrogen bonds, and the presence of higher CHOL concentrations enhanced the binding affinity (e.g., DPPC/DOPC/CHOL = 1:1:0, binding ratio = 0.114; DPPC/DOPC/CHOL = 1:1:1, binding ratio = 2.02). Compression isotherms indicated that the incorporation of 7S-peptides increased the DPPC/DOPC/CHOL monolayer fluidity and the lipid raft size. The presence of CHOL accelerated the 7S-peptide accumulation on lipid rafts, which could serve as platforms for peptides to develop into β-sheet rich structures. These results allow us to hypothesize that 7S-peptides may indirectly influence membrane protein functions via altering the membrane organization in the enterocytes.

  7. In situ investigation of dye adsorption on TiO2 films using a quartz crystal microbalance with a dissipation technique

    KAUST Repository

    Harms, Hauke A.

    2012-01-01

    Dye adsorption plays a crucial role in dye-sensitized solar cells. Herein, we demonstrate an in situ liquid-phase analytical technique to quantify in real time adsorption of dye and coadsorbates on flat and mesoporous TiO 2 films. For the first time, a molar ratio of co-adsorbed Y123 and chenodeoxycholic acid has been measured. © 2012 the Owner Societies.

  8. A PMMA coated PMN–PT single crystal resonator for sensing chemical agents

    International Nuclear Information System (INIS)

    Frank, Michael; Kassegne, Sam; Moon, Kee S

    2010-01-01

    A highly sensitive lead magnesium niobate–lead titanate (PMN–PT) single crystal resonator coated with a thin film of polymethylmethacrylate (PMMA) useful for detecting chemical agents such as acetone, methanol, and isopropyl alcohol is presented. Swelling of the cured PMMA polymer layer in the presence of acetone, methanol, and isopropyl alcohol vapors is sensed as a mass change transduced to an electrical signal by the PMN–PT thickness shear mode sensor. Frequency change in the PMN–PT sensor is demonstrated to vary according to the concentration of the chemical vapor present within the sensing chamber. For acetone, the results indicate a frequency change more than 6000 times greater than that which would be expected from a quartz crystal microbalance coated with PMMA. This study is the first of its kind to demonstrate vapor loading of adsorbed chemical agents onto a polymer coated PMN–PT resonator

  9. An oscillating microbalance for meteorological measurements of ice and volcanic ash accumulation from a weather balloon platform

    Science.gov (United States)

    Airey, Martin; Harrison, Giles; Nicoll, Keri; Williams, Paul; Marlton, Graeme

    2017-04-01

    A new, low cost, instrument has been developed for meteorological measurements of the accumulation of ice and volcanic ash that can be readily deployed using commercial radiosondes and weather balloons. It is based on principles used by [1], an instrument originally developed to measure supercooled liquid water profiles in clouds. This new instrument introduces numerous improvements in terms of reduced complexity and cost. It uses the oscillating microbalance principle, whereby a wire vibrating at its natural frequency is subjected to increased loading of the property to be measured. The increase in mass modifies the wire properties such that its natural frequency of oscillation changes. By measuring this frequency, the increase in mass can be inferred and transmitted to a ground base station through the radiosonde's UHF antenna via the PANDORA interface [2], which has been previously developed to provide power and connection to the radiosonde telemetry. The device consists of a simple circuit board controlled by an ATMEGA microcontroller. For calibration, the controller is capable of driving the wire at specified frequencies via excitation by a piezo sounder upon which the wire is mounted. The same piezo sounder is also used during active operation to measure the frequency of the wire in its non-driven state in order to infer the mass change on the wire. A phase-locked loop implemented on the board identifies when resonance occurs and the measured frequency is stable, prompting the microcontroller to send the measurement through the data interface. The device may be used for any application that requires the measurement of incremental mass variation e.g. ice accumulation, frosting, or particle accumulation such as dust and volcanic ash. For the solid particle accumulation, a low temperature, high-tack, adhesive may be applied to the wire prior to deployment to collect the material. In addition, the same instrument may be used for ground-based applications, such as

  10. Helium crystals

    International Nuclear Information System (INIS)

    Lipson, S.G.

    1987-01-01

    Hexagonal close-packed helium crystals in equilibrium with superfluid have been found to be one of the few systems in which an anisotropic solid comes into true thermodynamic equilibrium with its melt. The discovery of roughening transitions at the liquid-solid interface have shown this system to be ideal for the study of the statistical mechanics of interface structures. We describe the effect of roughening on the shape and growth of macroscopic crystals from both the theoretical and experimental points of view. (author)

  11. Microcantilver-based DNA hybridization sensors for Salmonella identification

    Directory of Open Access Journals (Sweden)

    Carlo Ricciardi

    2012-02-01

    Full Text Available The detection of pathogenic microorganisms in foods remains a challenging since the safety of foodstuffs has to be ensured by the food producing companies. Conventional methods for the detection and identification of bacteria mainly rely on specific microbiological and biochemical identification. Biomolecular methods, are commonly used as a support for traditional techniques, thanks to their high sensitivity, specificity and not excessive costs. However, new methods like biosensors for example, can be an exciting alternative to the more traditional tecniques for the detection of pathogens in food. In this study we report Salmonella enterica serotype Enteritidis DNA detection through a novel class of label-free biosensors: microcantilevers (MCs. In general, MCs can operate as a microbalance and is used to detect the mass of the entities anchored to the cantilever surface using the decrease in the resonant frequency. We use DNA hybridization as model reaction system and for this reason, specific single stranded probe DNA of the pathogen and three different DNA targets (single-stranded complementary DNA, PCR product and serial dilutions of DNA extracted from S. Enteritidis strains were applied. Two protocols were reported in order to allow the probe immobilization on cantilever surface: i MC surface was functionalized with 3-aminopropyltriethoxysilane and glutaraldehyde and an amino-modified DNA probe was used; ii gold-coated sensors and thiolated DNA probes were used in order to generate a covalent bonding (Th-Au. For the first one, measures after hybridization with the PCR product showed related frequency shift 10 times higher than hybridization with complementary probe and detectable signals were obtained at the concentrations of 103 and 106 cfu/mL after hybridization with bacterial DNA. There are currently optimizations of the second protocol, where preliminary results have shown to be more uniform and therefore more precise within each of the

  12. Magnetophotonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, M [Toyohashi University of Technology, Toyohashi, Aichi 441-8580 (Japan); Fujikawa, R [Toyohashi University of Technology, Toyohashi, Aichi 441-8580 (Japan); Baryshev, A [Toyohashi University of Technology, Toyohashi, Aichi 441-8580 (Japan); Khanikaev, A [Toyohashi University of Technology, Toyohashi, Aichi 441-8580 (Japan); Lim, P B [CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan (Japan); Uchida, H [Toyohashi University of Technology, Toyohashi, Aichi 441-8580 (Japan); Aktsipetrov, O [Lomonosov Moscow State University, Leninskie Gory, Moscow, 119992 (Russian Federation); Fedyanin, A [Lomonosov Moscow State University, Leninskie Gory, Moscow, 119992 (Russian Federation); Murzina, T [Lomonosov Moscow State University, Leninskie Gory, Moscow, 119992 (Russian Federation); Granovsky, A [Lomonosov Moscow State University, Leninskie Gory, Moscow, 119992 (Russian Federation)

    2006-04-21

    When the constitutive materials of photonic crystals (PCs) are magnetic, or even only a defect introduced in PCs is magnetic, the resultant PCs exhibit very unique optical and magneto-optical properties. The strong photon confinement in the vicinity of magnetic defects results in large enhancement in linear and nonlinear magneto-optical responses of the media. Novel functions, such as band Faraday effect, magnetic super-prism effect and non-reciprocal or magnetically controllable photonic band structure, are predicted to occur theoretically. All the unique features of the media arise from the existence of magnetization in media, and hence they are called magnetophotonic crystals providing the spin-dependent nature in PCs. (topical review)

  13. Magnetophotonic crystals

    International Nuclear Information System (INIS)

    Inoue, M; Fujikawa, R; Baryshev, A; Khanikaev, A; Lim, P B; Uchida, H; Aktsipetrov, O; Fedyanin, A; Murzina, T; Granovsky, A

    2006-01-01

    When the constitutive materials of photonic crystals (PCs) are magnetic, or even only a defect introduced in PCs is magnetic, the resultant PCs exhibit very unique optical and magneto-optical properties. The strong photon confinement in the vicinity of magnetic defects results in large enhancement in linear and nonlinear magneto-optical responses of the media. Novel functions, such as band Faraday effect, magnetic super-prism effect and non-reciprocal or magnetically controllable photonic band structure, are predicted to occur theoretically. All the unique features of the media arise from the existence of magnetization in media, and hence they are called magnetophotonic crystals providing the spin-dependent nature in PCs. (topical review)

  14. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  15. Dihydroxo-bridged dimeric Cu(II) system containing sandwiched non-coordinating phenylacetate anion: Crystal structure, spectroscopic, anti-bacterial, anti-fungal and DNA-binding studies of [(phen)(H2O)Cu(OH)2Cu(H2O)(phen)]2L.6H2O: (HL = phenylacetic acid; phen = 1,10-phenanthroline)

    Science.gov (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Shah, Naseer Ali

    2017-09-01

    This paper reports the synthesis, X-ray crystal structure, DNA-binding, antibacterial and antifungal studies of a rare dihydroxo-bridged dinuclear copper(II) complex including 1,10-phenanthroline (Phen) ligands and phenylacetate (L) anions, [Cu2(Phen)2(OH)2(H2O)2].2L.6H2O. Structural data revealed distorted square-pyramidal geometry for each copper(II) atom with the basal plane formed by the two nitrogen atoms of the phenantroline ligand and the oxygen atoms of two bridging hydroxyl groups. The apical positions are filled by the oxygen atom from a water molecule. This forms a centrosymmetric cationic dimer where the uncoordinated phenylacetate ligands serve to balance the electrical charge. The dimers interact by means of hydrogen bonds aided by the coordinated as well as uncoordinated water molecules and phenyl-acetate moieties in the crystal lattice. The binding ability of the complex with salmon sperm DNA was determined using cyclic voltammetry and absorption spectroscopy yielding binding constants 2.426 × 104 M-1 and 1.399 × 104 M-1, respectively. The complex was screened against two Gram-positive (Micrococcus luteus and Bacillus subtilis) and one Gram-negative (Escherichia coli) bacterial strains exhibiting significant activity against all the three strains. The complex exhibited significant, moderate and no activity against fungal strains Mucor piriformis, Helminthosporium solani and Aspergillus Niger, respectively. These preliminary tests indicate the competence of the complex towards the development of a potent biological drug.

  16. Improved understanding of protein complex offers insight into DNA

    Science.gov (United States)

    Summer Science Writing Internship Improved understanding of protein complex offers insight into DNA clearer understanding of the origin recognition complex (ORC) - a protein complex that directs DNA replication - through its crystal structure offers new insight into fundamental mechanisms of DNA replication

  17. Cloning and characterization of an insecticidal crystal protein gene ...

    Indian Academy of Sciences (India)

    Unknown

    The sequence of the cloned crystal protein gene showed almost complete homology with a mosquitocidal toxin gene from Bacillus .... diet or by topical application on food substrates as .... has very high similarity (99.74%) at DNA level with.

  18. Crystal structure of MboIIA methyltransferase.

    Science.gov (United States)

    Osipiuk, Jerzy; Walsh, Martin A; Joachimiak, Andrzej

    2003-09-15

    DNA methyltransferases (MTases) are sequence-specific enzymes which transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the amino group of either cytosine or adenine within a recognized DNA sequence. Methylation of a base in a specific DNA sequence protects DNA from nucleolytic cleavage by restriction enzymes recognizing the same DNA sequence. We have determined at 1.74 A resolution the crystal structure of a beta-class DNA MTase MboIIA (M.MboIIA) from the bacterium Moraxella bovis, the smallest DNA MTase determined to date. M.MboIIA methylates the 3' adenine of the pentanucleotide sequence 5'-GAAGA-3'. The protein crystallizes with two molecules in the asymmetric unit which we propose to resemble the dimer when M.MboIIA is not bound to DNA. The overall structure of the enzyme closely resembles that of M.RsrI. However, the cofactor-binding pocket in M.MboIIA forms a closed structure which is in contrast to the open-form structures of other known MTases.

  19. Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

    Science.gov (United States)

    Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

    2015-10-01

    Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues

  20. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  1. Photonic time crystals.

    Science.gov (United States)

    Zeng, Lunwu; Xu, Jin; Wang, Chengen; Zhang, Jianhua; Zhao, Yuting; Zeng, Jing; Song, Runxia

    2017-12-07

    When space (time) translation symmetry is spontaneously broken, the space crystal (time crystal) forms; when permittivity and permeability periodically vary with space (time), the photonic crystal (photonic time crystal) forms. We proposed the concept of photonic time crystal and rewritten the Maxwell's equations. Utilizing Finite Difference Time Domain (FDTD) method, we simulated electromagnetic wave propagation in photonic time crystal and photonic space-time crystal, the simulation results show that more intensive scatter fields can obtained in photonic time crystal and photonic space-time crystal.

  2. Photonic Crystal Fibers

    National Research Council Canada - National Science Library

    Kristiansen, Rene E

    2005-01-01

    This report results from a contract tasking Crystal Fibre A/S as follows: Crystal Fibre will conduct research and development of large mode area, dual clad multi-core Yb-doped photonic crystal fiber...

  3. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  4. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  5. Measurements of DNA Damage and Repair in Bacillus anthracis Sterne Spores by UV Radiation

    Science.gov (United States)

    2014-09-18

    tightly into chromosomal structure, which serves to protect the DNA. The DNA is coiled several times and wrapped tightly around proteins. The wrapping...helps the DNA keep its chromatin structure. When DNA is to be replicated, enzymes unwind the chromosomal DNA. Therefore, DNA is not specifically used...2 See Appendix for Plasmid Information sheet. 30 the ice crystals disappeared . The tube was gently mixed by hand

  6. Novel DNA materials and their applications.

    Science.gov (United States)

    Yang, Dayong; Campolongo, Michael J; Nhi Tran, Thua Nguyen; Ruiz, Roanna C H; Kahn, Jason S; Luo, Dan

    2010-01-01

    The last two decades have witnessed the exponential development of DNA as a generic material instead of just a genetic material. The biological function, nanoscale geometry, biocompatibility, biodegradability, and molecular recognition capacity of DNA make it a promising candidate for the construction of novel functional nanomaterials. As a result, DNA has been recognized as one of the most appealing and versatile nanomaterial building blocks. Scientists have used DNA in this way to construct various amazing nanostructures, such as ordered lattices, origami, supramolecular assemblies, and even three-dimensional objects. In addition, DNA has been utilized as a guide and template to direct the assembly of other nanomaterials including nanowires, free-standing membranes, and crystals. Furthermore, DNA can also be used as structural components to construct bulk materials such as DNA hydrogels, demonstrating its ability to behave as a unique polymer. Overall, these novel DNA materials have found applications in various areas in the biomedical field in general, and nanomedicine in particular. In this review, we summarize the development of DNA assemblies, describe the innovative progress of multifunctional and bulk DNA materials, and highlight some real-world nanomedical applications of these DNA materials. We also show our insights throughout this article for the future direction of DNA materials. © 2010 John Wiley & Sons, Inc.

  7. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  8. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  9. In-silico investigations into natural products as nonnucleoside DNA ...

    African Journals Online (AJOL)

    nucleoside DNA methyltransferase 1 (DNMT1) inhibitor of epimutation in gastric cancer. Methods: A dataset of reported non-nucleoside DNMT1 inhibitors was used to target the active site of crystallized DNMT1 protein. Molecular docking simulations ...

  10. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  11. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  12. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  13. Regular square planer bis-(4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione)/copper(II) complex: Trans/cis-DFT isomerization, crystal structure, thermal, solvatochromism, hirshfeld surface and DNA-binding analysis

    Science.gov (United States)

    Hema, M. K.; Karthik, C. S.; Warad, Ismail; Lokanath, N. K.; Zarrouk, Abdelkader; Kumara, Karthik; Pampa, K. J.; Mallu, P.

    2018-04-01

    Trans-[Cu(O∩O)2] complex, O∩O = 4,4,4-trifluoro-1-(thiophen-2-yl)butane-1,3-dione was reported with high potential toward CT-DNA binder. The solved XRD-structure of complex indicated a perfect regular square-planer geometry around the Cu(II) center. The trans/cis-DFT-isomerization calculation supported the XRD seen in reflecting the trans-isomer as the kinetic-favor isomer. The desired complex structure was also characterized by conductivity measurement, CHN-elemental analyses, MS, EDX, SEM, UV-Vis., FT-IR, HAS and TG/DTG. The Solvatochromism behavior of the complex was evaluated using four different polar solvents. MPE and Hirshfeld surface analysis (HSA) come to an agreement that fluoride and thiophene protons atoms are with suitable electro-potential environment to form non-classical H-bonds of type CThsbnd H⋯F. The DNA-binding properties were investigated by viscosity tests and spectrometric titrations, the results revealed the complex as strong calf-thymus DNA binder. High intrinsic-binding constants value ∼1.8 × 105 was collected.

  14. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  15. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un [Ithaca, NY; Gruner, Sol M [Ithaca, NY

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  16. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  17. Mechanism of Error-Free DNA Replication Past Lucidin-Derived DNA Damage by Human DNA Polymerase κ.

    Science.gov (United States)

    Yockey, Oliver P; Jha, Vikash; Ghodke, Pratibha P; Xu, Tianzuo; Xu, Wenyan; Ling, Hong; Pradeepkumar, P I; Zhao, Linlin

    2017-11-20

    DNA damage impinges on genetic information flow and has significant implications in human disease and aging. Lucidin-3-O-primeveroside (LuP) is an anthraquinone derivative present in madder root, which has been used as a coloring agent and food additive. LuP can be metabolically converted to genotoxic compound lucidin, which subsequently forms lucidin-specific N 2 -2'-deoxyguanosine (N 2 -dG) and N 6 -2'-deoxyadenosine (N 6 -dA) DNA adducts. Lucidin is mutagenic and carcinogenic in rodents but has low carcinogenic risks in humans. To understand the molecular mechanism of low carcinogenicity of lucidin in humans, we performed DNA replication assays using site-specifically modified oligodeoxynucleotides containing a structural analogue (LdG) of lucidin-N 2 -dG DNA adduct and determined the crystal structures of DNA polymerase (pol) κ in complex with LdG-bearing DNA and an incoming nucleotide. We examined four human pols (pol η, pol ι, pol κ, and Rev1) in their efficiency and accuracy during DNA replication with LdG; these pols are key players in translesion DNA synthesis. Our results demonstrate that pol κ efficiently and accurately replicates past the LdG adduct, whereas DNA replication by pol η, pol ι is compromised to different extents. Rev1 retains its ability to incorporate dCTP opposite the lesion albeit with decreased efficiency. Two ternary crystal structures of pol κ illustrate that the LdG adduct is accommodated by pol κ at the enzyme active site during insertion and postlesion-extension steps. The unique open active site of pol κ allows the adducted DNA to adopt a standard B-form for accurate DNA replication. Collectively, these biochemical and structural data provide mechanistic insights into the low carcinogenic risk of lucidin in humans.

  18. CRYSTALLIZATION IN MULTICOMPONENT GLASSES

    Energy Technology Data Exchange (ETDEWEB)

    KRUGER AA; HRMA PR

    2009-10-08

    In glass processing situations involving glass crystallization, various crystalline forms nucleate, grow, and dissolve, typically in a nonuniform temperature field of molten glass subjected to convection. Nuclear waste glasses are remarkable examples of multicomponent vitrified mixtures involving partial crystallization. In the glass melter, crystals form and dissolve during batch-to-glass conversion, melter processing, and product cooling. Crystals often agglomerate and sink, and they may settle at the melter bottom. Within the body of cooling glass, multiple phases crystallize in a non-uniform time-dependent temperature field. Self-organizing periodic distribution (the Liesegnang effect) is common. Various crystallization phenomena that occur in glass making are reviewed.

  19. Crystallization In Multicomponent Glasses

    International Nuclear Information System (INIS)

    Kruger, A.A.; Hrma, P.R.

    2009-01-01

    In glass processing situations involving glass crystallization, various crystalline forms nucleate, grow, and dissolve, typically in a nonuniform temperature field of molten glass subjected to convection. Nuclear waste glasses are remarkable examples of multicomponent vitrified mixtures involving partial crystallization. In the glass melter, crystals form and dissolve during batch-to-glass conversion, melter processing, and product cooling. Crystals often agglomerate and sink, and they may settle at the melter bottom. Within the body of cooling glass, multiple phases crystallize in a non-uniform time-dependent temperature field. Self-organizing periodic distribution (the Liesegnang effect) is common. Various crystallization phenomena that occur in glass making are reviewed.

  20. Synthesis, spectroscopic and DNA binding ability of Co{sup II}, Ni{sup II}, Cu{sup II} and Zn{sup II} complexes of Schiff base ligand (E)-1-(((1H-benzo[d]imidazol-2-yl)methylimino)methyl)naphthalen-2-ol. X-ray crystal structure determination of cobalt (II) complex

    Energy Technology Data Exchange (ETDEWEB)

    Yarkandi, Naeema H. [Chemistry Department, Faculty of Applied Science, Umm Al–Qura University, Makkah (Saudi Arabia); El-Ghamry, Hoda A., E-mail: helghamrymo@yahoo.com [Chemistry Department, Faculty of Applied Science, Umm Al–Qura University, Makkah (Saudi Arabia); Chemistry Department, Faculty of Science, Tanta University, Tanta (Egypt); Gaber, Mohamed [Chemistry Department, Faculty of Science, Tanta University, Tanta (Egypt)

    2017-06-01

    A novel Schiff base ligand, (E)-1-(((1H-benzo[d]imidazol-2-yl)methylimino)methyl)naphthalen-2-ol (HL), has been designed and synthesized in addition to its metal chelates [Co(L){sub 2}]·l2H{sub 2}O, [Ni(L)Cl·(H{sub 2}O){sub 2}].5H{sub 2}O, [Cu(L)Cl] and [Zn(L)(CH{sub 3}COO)]. The structures of the isolated compounds have been confirmed and identified by means of different spectral and physicochemical techniques including CHN analysis, {sup 1}H &{sup 13}C NMR, mass spectral analysis, molar conductivity measurement, UV–Vis, infrared, magnetic moment in addition to TGA technique. The infrared spectral results ascertained that the ligand acts as monobasic tridentate binding to the metal centers via deprotonated hydroxyl oxygen, azomethine and imidazole nitrogen atoms. The UV–Vis, magnetic susceptibility and molar conductivity data implied octahedral geometry for Co(II) & Ni(II) complexes, tetrahedral for Zn(II) complex and square planar for Cu(II) complex. X-ray structural analysis of Co(II) complex 1 has been reported and discussed. Moreover, the type of interaction between the ligand & its complexes towards salmon sperm DNA (SS-DNA) has been examined by the measurement of absorption spectra and viscosity which confirmed that the ligand and its complexes interact with DNA via intercalation interaction as concluded from the values of binding constants (K{sub b}). - Highlights: • Synthesis of Co{sup II}, Ni{sup II}, Cu{sup II} and Zn{sup II} complexes of the Schiff base ligand based on 2-(aminomethyl)benzimidazole moiety. • The constitutions and structures of the ligand and complexes were elucidated. • Molecular structure of Co{sup II} complex was confirmed by single crystal X-ray diffraction method. • The ligand and its complexes interact with SS-DNA via intercalation mods.

  1. DNA hydration studied by neutron fiber diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J. [Keele Univ. (United Kingdom)] [and others

    1994-12-31

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix.

  2. DNA hydration studied by neutron fiber diffraction

    International Nuclear Information System (INIS)

    Fuller, W.; Forsyth, V.T.; Mahendrasingam, A.; Langan, P.; Pigram, W.J.

    1994-01-01

    The development of neutron high angle fiber diffraction to investigate the location of water around the deoxyribonucleic acid (DNA) double-helix is described. The power of the technique is illustrated by its application to the D and A conformations of DNA using the single crystal diffractometer, D19, at the Institute Laue-Langevin, Grenoble and the time of flight diffractometer, SXD, at the Rutherford Appleton ISIS Spallation Neutron Source. These studies show the existence of bound water closely associated with the DNA. The patterns of hydration in these two DNA conformations are quite distinct and are compared to those observed in X-ray single crystal studies of two-stranded oligodeoxynucleotides. Information on the location of water around the DNA double-helix from the neutron fiber diffraction studies is combined with that on the location of alkali metal cations from complementary X-ray high angle fiber diffraction studies at the Daresbury Laboratory SRS using synchrotron radiation. These analyses emphasize the importance of viewing DNA, water and ions as a single system with specific interactions between the three components and provide a basis for understanding the effect of changes in the concentration of water and ions in inducing conformations] transitions in the DNA double-helix

  3. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  4. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  5. Photonic crystal pioneer

    Science.gov (United States)

    Anscombe, Nadya

    2011-08-01

    Over the past ten years, Crystal Fiber, now part of NKT Photonics, has been busy commercializing photonic crystal fibre. Nadya Anscombe finds out about the evolution of the technology and its applications.

  6. Crystallization Pathways in Biomineralization

    Science.gov (United States)

    Weiner, Steve; Addadi, Lia

    2011-08-01

    A crystallization pathway describes the movement of ions from their source to the final product. Cells are intimately involved in biological crystallization pathways. In many pathways the cells utilize a unique strategy: They temporarily concentrate ions in intracellular membrane-bound vesicles in the form of a highly disordered solid phase. This phase is then transported to the final mineralization site, where it is destabilized and crystallizes. We present four case studies, each of which demonstrates specific aspects of biological crystallization pathways: seawater uptake by foraminifera, calcite spicule formation by sea urchin larvae, goethite formation in the teeth of limpets, and guanine crystal formation in fish skin and spider cuticles. Three representative crystallization pathways are described, and aspects of the different stages of crystallization are discussed. An in-depth understanding of these complex processes can lead to new ideas for synthetic crystallization processes of interest to materials science.

  7. Photonic Crystal Nanocavity Arrays

    National Research Council Canada - National Science Library

    Altug, Hatice; Vuckovic, Jelena

    2006-01-01

    We recently proposed two-dimensional coupled photonic crystal nanocavity arrays as a route to achieve a slow-group velocity of light in all crystal directions, thereby enabling numerous applications...

  8. Growth of dopamine crystals

    Energy Technology Data Exchange (ETDEWEB)

    Patil, Vidya, E-mail: vidya.patil@ruparel.edu; Patki, Mugdha, E-mail: mugdha.patki@ruparel.edu [D. G. Ruparel College, Senapati Bapat Marg, Mahim, Mumbai – 400 016 (India)

    2016-05-06

    Many nonlinear optical (NLO) crystals have been identified as potential candidates in optical and electro-optical devices. Use of NLO organic crystals is expected in photonic applications. Hence organic nonlinear optical materials have been intensely investigated due to their potentially high nonlinearities, and rapid response in electro-optic effect compared to inorganic NLO materials. There are many methods to grow organic crystals such as vapor growth method, melt growth method and solution growth method. Out of these methods, solution growth method is useful in providing constraint free crystal. Single crystals of Dopamine have been grown by evaporating the solvents from aqueous solution. Crystals obtained were of the size of orders of mm. The crystal structure of dopamine was determined using XRD technique. Images of crystals were obtained using FEG SEM Quanta Series under high vacuum and low KV.

  9. DNA-imprinted polymer nanoparticles with monodispersity and prescribed DNA-strand patterns

    Science.gov (United States)

    Trinh, Tuan; Liao, Chenyi; Toader, Violeta; Barłóg, Maciej; Bazzi, Hassan S.; Li, Jianing; Sleiman, Hanadi F.

    2018-02-01

    As colloidal self-assembly increasingly approaches the complexity of natural systems, an ongoing challenge is to generate non-centrosymmetric structures. For example, patchy, Janus or living crystallization particles have significantly advanced the area of polymer assembly. It has remained difficult, however, to devise polymer particles that associate in a directional manner, with controlled valency and recognition motifs. Here, we present a method to transfer DNA patterns from a DNA cage to a polymeric nanoparticle encapsulated inside the cage in three dimensions. The resulting DNA-imprinted particles (DIPs), which are 'moulded' on the inside of the DNA cage, consist of a monodisperse crosslinked polymer core with a predetermined pattern of different DNA strands covalently 'printed' on their exterior, and further assemble with programmability and directionality. The number, orientation and sequence of DNA strands grafted onto the polymeric core can be controlled during the process, and the strands are addressable independently of each other.

  10. Apparatus for mounting crystal

    Science.gov (United States)

    Longeway, Paul A.

    1985-01-01

    A thickness monitor useful in deposition or etching reactor systems comprising a crystal-controlled oscillator in which the crystal is deposited or etched to change the frequency of the oscillator. The crystal rests within a thermally conductive metallic housing and arranged to be temperature controlled. Electrode contacts are made to the surface primarily by gravity force such that the crystal is substantially free of stress otherwise induced by high temperature.

  11. ALICE photon spectrometer crystals

    CERN Multimedia

    Maximilien Brice

    2006-01-01

    Members of the mechanical assembly team insert the last few crystals into the first module of ALICE's photon spectrometer. These crystals are made from lead-tungstate, a crystal as clear as glass but with nearly four times the density. When a high-energy particle passes through one of these crystals it will scintillate, emitting a flash of light allowing the energy of photons, electrons and positrons to be measured.

  12. Crystal Growth Technology

    Science.gov (United States)

    Scheel, Hans J.; Fukuda, Tsuguo

    2004-06-01

    This volume deals with the technologies of crystal fabrication, of crystal machining, and of epilayer production and is the first book on industrial and scientific aspects of crystal and layer production. The major industrial crystals are treated: Si, GaAs, GaP, InP, CdTe, sapphire, oxide and halide scintillator crystals, crystals for optical, piezoelectric and microwave applications and more. Contains 29 contributions from leading crystal technologists covering the following topics: General aspects of crystal growth technology Silicon Compound semiconductors Oxides and halides Crystal machining Epitaxy and layer deposition Scientific and technological problems of production and machining of industrial crystals are discussed by top experts, most of them from the major growth industries and crystal growth centers. In addition, it will be useful for the users of crystals, for teachers and graduate students in materials sciences, in electronic and other functional materials, chemical and metallurgical engineering, micro-and optoelectronics including nanotechnology, mechanical engineering and precision-machining, microtechnology, and in solid-state sciences.

  13. Food crystallization and eggs.

    Science.gov (United States)

    Egg products can be utilized to control crystallization in a diverse realm of food products. Albumen and egg yolk can aid in the control of sugar crystal formation in candies. Egg yolk can enhance the textural properties and aid in the control of large ice crystal formation in frozen desserts. In...

  14. [Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment].

    Science.gov (United States)

    Akberova, N I; Zhmurov, A A; Nevzorova, T A; Litvinov, R I

    2016-01-01

    Antibodies to DNA play an important role in the pathogenesis of autoimmune diseases. The elucidation of structural mechanisms of both the antigen recognition and the interaction of anti-DNA antibodies with DNA will help to understand the role of DNA-containing immune complexes in various pathologies and can provide a basis for new treatment modalities. Moreover, the DNA-antibody complex is an analog of specific intracellular DNA-protein interactions. In this work, we used in silico molecular dynamic simulations of bimolecular complexes of the dsDNA segment containing the Fab fragment of an anti-DNA antibody to obtain the detailed thermodynamic and structural characteristics of dynamic intermolecular interactions. Using computationally modified crystal structure of the Fab-DNA complex (PDB ID: 3VW3), we studied the equilibrium molecular dynamics of the 64M-5 antibody Fab fragment associated with the dsDNA fragment containing the thymine dimer, the product of DNA photodamage. Amino acid residues that constitute paratopes and the complementary nucleotide epitopes for the Fab-DNA construct were identified. Stacking and electrostatic interactions were found to play the main role in mediating the most specific antibody-dsDNA contacts, while hydrogen bonds were less significant. These findings may shed light on the formation and properties of pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus associated with skin photosensitivity and DNA photodamage.

  15. DNA repair

    International Nuclear Information System (INIS)

    Setlow, R.

    1978-01-01

    Some topics discussed are as follows: difficulty in extrapolating data from E. coli to mammalian systems; mutations caused by UV-induced changes in DNA; mutants deficient in excision repair; other postreplication mechanisms; kinds of excision repair systems; detection of repair by biochemical or biophysical means; human mutants deficient in repair; mutagenic effects of UV on XP cells; and detection of UV-repair defects among XP individuals

  16. Molecular dynamics simulations of DNA-free and DNA-bound TAL effectors.

    Directory of Open Access Journals (Sweden)

    Hua Wan

    Full Text Available TAL (transcriptional activator-like effectors (TALEs are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA, the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL. The conformational analysis of DNA indicates that the 5' end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism.

  17. Protein Crystal Growth

    Science.gov (United States)

    2003-01-01

    In order to rapidly and efficiently grow crystals, tools were needed to automatically identify and analyze the growing process of protein crystals. To meet this need, Diversified Scientific, Inc. (DSI), with the support of a Small Business Innovation Research (SBIR) contract from NASA s Marshall Space Flight Center, developed CrystalScore(trademark), the first automated image acquisition, analysis, and archiving system designed specifically for the macromolecular crystal growing community. It offers automated hardware control, image and data archiving, image processing, a searchable database, and surface plotting of experimental data. CrystalScore is currently being used by numerous pharmaceutical companies and academic and nonprofit research centers. DSI, located in Birmingham, Alabama, was awarded the patent Method for acquiring, storing, and analyzing crystal images on March 4, 2003. Another DSI product made possible by Marshall SBIR funding is VaporPro(trademark), a unique, comprehensive system that allows for the automated control of vapor diffusion for crystallization experiments.

  18. Photonic crystal light source

    Science.gov (United States)

    Fleming, James G [Albuquerque, NM; Lin, Shawn-Yu [Albuquerque, NM; Bur, James A [Corrales, NM

    2004-07-27

    A light source is provided by a photonic crystal having an enhanced photonic density-of-states over a band of frequencies and wherein at least one of the dielectric materials of the photonic crystal has a complex dielectric constant, thereby producing enhanced light emission at the band of frequencies when the photonic crystal is heated. The dielectric material can be a metal, such as tungsten. The spectral properties of the light source can be easily tuned by modification of the photonic crystal structure and materials. The photonic crystal light source can be heated electrically or other heating means. The light source can further include additional photonic crystals that exhibit enhanced light emission at a different band of frequencies to provide for color mixing. The photonic crystal light source may have applications in optical telecommunications, information displays, energy conversion, sensors, and other optical applications.

  19. The structure of DNA by direct imaging

    KAUST Repository

    Marini, Monica; Falqui, Andrea; Moretti, Manola; Limongi, Tania; Allione, Marco; Genovese, Alessandro; Lopatin, Sergei; Tirinato, Luca; Das, Gobind; Torre, Bruno; Giugni, Andrea; Gentile, Francesco; Candeloro, Patrizio; Di Fabrizio, Enzo M.

    2015-01-01

    The structure of DNA was determined in 1953 by x-ray fiber diffraction. Several attempts have been made to obtain a direct image of DNA with alternative techniques. The direct image is intended to allow a quantitative evaluation of all relevant characteristic lengths present in a molecule. A direct image of DNA, which is different from diffraction in the reciprocal space, is difficult to obtain for two main reasons: the intrinsic very low contrast of the elements that form the molecule and the difficulty of preparing the sample while preserving its pristine shape and size. We show that through a preparation procedure compatible with the DNA physiological conditions, a direct image of a single suspended DNA molecule can be obtained. In the image, all relevant lengths of A-form DNA are measurable. A high-resolution transmission electron microscope that operates at 80 keV with an ultimate resolution of 1.5 Å was used for this experiment. Direct imaging of a single molecule can be used as a method to address biological problems that require knowledge at the single-molecule level, given that the average information obtained by x-ray diffraction of crystals or fibers is not sufficient for detailed structure determination, or when crystals cannot be obtained from biological molecules or are not sufficient in understanding multiple protein configurations.

  20. The structure of DNA by direct imaging

    KAUST Repository

    Marini, Monica

    2015-08-28

    The structure of DNA was determined in 1953 by x-ray fiber diffraction. Several attempts have been made to obtain a direct image of DNA with alternative techniques. The direct image is intended to allow a quantitative evaluation of all relevant characteristic lengths present in a molecule. A direct image of DNA, which is different from diffraction in the reciprocal space, is difficult to obtain for two main reasons: the intrinsic very low contrast of the elements that form the molecule and the difficulty of preparing the sample while preserving its pristine shape and size. We show that through a preparation procedure compatible with the DNA physiological conditions, a direct image of a single suspended DNA molecule can be obtained. In the image, all relevant lengths of A-form DNA are measurable. A high-resolution transmission electron microscope that operates at 80 keV with an ultimate resolution of 1.5 Å was used for this experiment. Direct imaging of a single molecule can be used as a method to address biological problems that require knowledge at the single-molecule level, given that the average information obtained by x-ray diffraction of crystals or fibers is not sufficient for detailed structure determination, or when crystals cannot be obtained from biological molecules or are not sufficient in understanding multiple protein configurations.

  1. DNA repair

    International Nuclear Information System (INIS)

    Van Zeeland, A.A.

    1984-01-01

    In this chapter a series of DNA repair pathways are discussed which are available to the cell to cope with the problem of DNA damaged by chemical or physical agents. In the case of microorganisms our knowledge about the precise mechanism of each DNA repair pathway and the regulation of it has been improved considerably when mutants deficient in these repair mechanisms became available. In the case of mammalian cells in culture, until recently there were very little repair deficient mutants available, because in almost all mammalian cells in culture at least the diploid number of chromosomes is present. Therefore the frequency of repair deficient mutants in such populations is very low. Nevertheless because replica plating techniques are improving some mutants from Chinese hamsters ovary cells and L5178Y mouse lymphoma cells are now available. In the case of human cells, cultures obtained from patients with certain genetic diseases are available. A number of cells appear to be sensitive to some chemical or physical mutagens. These include cells from patients suffering from xeroderma pigmentosum, Ataxia telangiectasia, Fanconi's anemia, Cockayne's syndrome. However, only in the case of xeroderma pigmentosum cells, has the sensitivity to ultraviolet light been clearly correlated with a deficiency in excision repair of pyrimidine dimers. Furthermore the work with strains obtained from biopsies from man is difficult because these cells generally have low cloning efficiencies and also have a limited lifespan in vitro. It is therefore very important that more repair deficient mutants will become available from established cell lines from human or animal origin

  2. Photonic Crystal Biosensor Chip for Label-Free Detection of Bacteria

    DEFF Research Database (Denmark)

    Kristensen, Martin; Krüger, Asger Christian; Groothoff, Nathaniel

    Narrow polarization-mixing resonances in planar photonic crystals are studied as candidate components for label-free refractive index sensors for detecting bacteria causing sepsis through the identification of DNA strands....

  3. Dew Point Calibration System Using a Quartz Crystal Sensor with a Differential Frequency Method

    Directory of Open Access Journals (Sweden)

    Ningning Lin

    2016-11-01

    Full Text Available In this paper, the influence of temperature on quartz crystal microbalance (QCM sensor response during dew point calibration is investigated. The aim is to present a compensation method to eliminate temperature impact on frequency acquisition. A new sensitive structure is proposed with double QCMs. One is kept in contact with the environment, whereas the other is not exposed to the atmosphere. There is a thermal conductivity silicone pad between each crystal and a refrigeration device to keep a uniform temperature condition. A differential frequency method is described in detail and is applied to calibrate the frequency characteristics of QCM at the dew point of −3.75 °C. It is worth noting that frequency changes of two QCMs were approximately opposite when temperature conditions were changed simultaneously. The results from continuous experiments show that the frequencies of two QCMs as the dew point moment was reached have strong consistency and high repeatability, leading to the conclusion that the sensitive structure can calibrate dew points with high reliability.

  4. Dew Point Calibration System Using a Quartz Crystal Sensor with a Differential Frequency Method.

    Science.gov (United States)

    Lin, Ningning; Meng, Xiaofeng; Nie, Jing

    2016-11-18

    In this paper, the influence of temperature on quartz crystal microbalance (QCM) sensor response during dew point calibration is investigated. The aim is to present a compensation method to eliminate temperature impact on frequency acquisition. A new sensitive structure is proposed with double QCMs. One is kept in contact with the environment, whereas the other is not exposed to the atmosphere. There is a thermal conductivity silicone pad between each crystal and a refrigeration device to keep a uniform temperature condition. A differential frequency method is described in detail and is applied to calibrate the frequency characteristics of QCM at the dew point of -3.75 °C. It is worth noting that frequency changes of two QCMs were approximately opposite when temperature conditions were changed simultaneously. The results from continuous experiments show that the frequencies of two QCMs as the dew point moment was reached have strong consistency and high repeatability, leading to the conclusion that the sensitive structure can calibrate dew points with high reliability.

  5. Scintillation crystal mounting apparatus

    International Nuclear Information System (INIS)

    Engdahl, L.W.; Deans, A.J.

    1982-01-01

    An improved detector head for a gamma camera is disclosed. The detector head includes a housing and a detector assembly mounted within the housing. Components of the detector assembly include a crystal sub-assembly, a phototube array, and a light pipe between the phototube array and crystal sub-assembly. The invention provides a unique structure for maintaining the phototubes in optical relationship with the light pipe and preventing the application of forces that would cause the camera's crystal to crack

  6. CMS lead tungstate crystals

    CERN Multimedia

    Laurent Guiraud

    2000-01-01

    These crystals are made from lead tungstate, a crystal that is as clear as glass yet with nearly four times the density. They have been produced in Russia to be used as scintillators in the electromagnetic calorimeter on the CMS experiment, part of the LHC project at CERN. When an electron, positron or photon passes through the calorimeter it will cause a cascade of particles that will then be absorbed by these scintillating crystals, allowing the particle's energy to be measured.

  7. Macromolecular crystallization in microgravity

    International Nuclear Information System (INIS)

    Snell, Edward H; Helliwell, John R

    2005-01-01

    Density difference fluid flows and sedimentation of growing crystals are greatly reduced when crystallization takes place in a reduced gravity environment. In the case of macromolecular crystallography a crystal of a biological macromolecule is used for diffraction experiments (x-ray or neutron) so as to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal then the greater the molecular structure detail that can be extracted. It is this structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences, with major potential in understanding disease pathologies. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyse the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry and mathematics meet to enable insight to the fundamentals of life. As the reader will see, there is a great deal of physics involved when the microgravity environment is applied to crystallization, some of it known, and undoubtedly much yet to

  8. Bio-recognitive photonics of a DNA-guided organic semiconductor

    Science.gov (United States)

    Back, Seung Hyuk; Park, Jin Hyuk; Cui, Chunzhi; Ahn, Dong June

    2016-01-01

    Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA-DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distribution of the DNA molecules with a shape of an `inverted' hourglass. The crystal's luminescent intensity is enhanced by 1.6-fold upon recognition of the perfect-matched target DNA sequence, but not in the case of a single-base mismatched one. The DNA-DNA recognition forming double-helix structure is identified to occur only in the rod's outer periphery. This study opens up new opportunities of Alq3, one of the most widely used OLED materials, enabling biological recognition.

  9. Bio-recognitive photonics of a DNA-guided organic semiconductor.

    Science.gov (United States)

    Back, Seung Hyuk; Park, Jin Hyuk; Cui, Chunzhi; Ahn, Dong June

    2016-01-04

    Incorporation of duplex DNA with higher molecular weights has attracted attention for a new opportunity towards a better organic light-emitting diode (OLED) capability. However, biological recognition by OLED materials is yet to be addressed. In this study, specific oligomeric DNA-DNA recognition is successfully achieved by tri (8-hydroxyquinoline) aluminium (Alq3), an organic semiconductor. Alq3 rods crystallized with guidance from single-strand DNA molecules show, strikingly, a unique distribution of the DNA molecules with a shape of an 'inverted' hourglass. The crystal's luminescent intensity is enhanced by 1.6-fold upon recognition of the perfect-matched target DNA sequence, but not in the case of a single-base mismatched one. The DNA-DNA recognition forming double-helix structure is identified to occur only in the rod's outer periphery. This study opens up new opportunities of Alq3, one of the most widely used OLED materials, enabling biological recognition.

  10. Active Photonic Crystal Waveguides

    DEFF Research Database (Denmark)

    Ek, Sara

    This thesis deals with the fabrication and characterization of active photonic crystal waveguides, realized in III-V semiconductor material with embedded active layers. The platform offering active photonic crystal waveguides has many potential applications. One of these is a compact photonic...... due to photonic crystal dispersion. The observations are explained by the enhancement of net gain by light slow down. Another application based on active photonic crystal waveguides is micro lasers. Measurements on quantum dot micro laser cavities with different mirror configurations and photonic...

  11. A crystal barrel

    CERN Multimedia

    2007-01-01

    The production of crystals for the barrel of the CMS electromagnetic calorimeter has been completed. This is an important milestone for the experiment, which received the last of its 62,960 crystals on 9 March. The members of the team responsible for the crystal acceptance testing at CERN display the last crystal for the CMS electromagnetic calorimeter barrel. From left to right: Igor Tarasov, Etiennette Auffray and Hervé Cornet.One of the six machines specially developed to measure 67 different parameters on each crystal. Igor Tarasov is seen inserting the last batch of crystals into the machine. The last of the 62,960 CMS barrel crystals arrived at CERN on 9 March. Once removed from its polystyrene protection, this delicate crystal, like thousands of its predecessors, will be inserted into the last of the 36 supermodules of the barrel electromagnetic calorimeter in a few days' time. This marks the end of an important chapter in an almost 15-year-long journey by the CMS crystals team, some of whose member...

  12. Automation in biological crystallization.

    Science.gov (United States)

    Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

    2014-06-01

    Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

  13. Crystallization Formulation Lab

    Data.gov (United States)

    Federal Laboratory Consortium — The Crystallization Formulation Lab fills a critical need in the process development and optimization of current and new explosives and energetic formulations. The...

  14. Highly crystallized nanometer-sized zeolite a with large Cs adsorption capability for the decontamination of water.

    Science.gov (United States)

    Torad, Nagy L; Naito, Masanobu; Tatami, Junichi; Endo, Akira; Leo, Sin-Yen; Ishihara, Shinsuke; Wu, Kevin C-W; Wakihara, Toru; Yamauchi, Yusuke

    2014-03-01

    Nanometer-sized zeolite A with a large cesium (Cs) uptake capability is prepared through a simple post-milling recrystallization method. This method is suitable for producing nanometer-sized zeolite in large scale, as additional organic compounds are not needed to control zeolite nucleation and crystal growth. Herein, we perform a quartz crystal microbalance (QCM) study to evaluate the uptake ability of Cs ions by zeolite, to the best of our knowledge, for the first time. In comparison to micrometer-sized zeolite A, nanometer-sized zeolite A can rapidly accommodate a larger amount of Cs ions into the zeolite crystal structure, owing to its high external surface area. Nanometer-sized zeolite is a promising candidate for the removal of radioactive Cs ions from polluted water. Our QCM study on Cs adsorption uptake behavior provides the information of adsorption kinetics (e.g., adsorption amounts and rates). This technique is applicable to other zeolites, which will be highly valuable for further consideration of radioactive Cs removal in the future. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Preparation and characterization of PTFE coating in new polymer quartz piezoelectric crystal sensor for testing liquor products

    International Nuclear Information System (INIS)

    Gu Yu; Li Qiang

    2015-01-01

    A new method was developed based on the electron beam vacuum dispersion (EBVD) technology to prepare the PTFE polymer coating of the new polymer quartz piezoelectric crystal sensor for testing liquor products. The new method was applied in the new EBVD equipment which we designed. A real-time system monitoring the polymer coating’s thickness was designed for the new EBVD equipment according to the quartz crystal microbalance (QCM) principle, playing an important role in preparing stable and uniform PTFE polymer coatings of the same thickness. 30 pieces of PTFE polymer coatings on the surface of the quartz crystal basis were prepared with the PTFE polymer ultrafine powder (purity ≥ 99.99%) as the starting material. We obtained 30 pieces of new PTFE polymer sensors. By using scanning electron microscopy (SEM), the structure of the PTFE polymer coating’s column clusters was studied. One sample from the 30 pieces of new PTFE polymer sensors was analysed by SEM in four scales, i.e., 400×, 1000×, 10000×, and 25000×. It was shown that under the condition of high bias voltage and low bias current, uniformly PTFE polymer coating could be achieved, which indicates that the new EBVD equipment is suitable for mass production of stable and uniform polymer coating. (paper)

  16. Thermotropic Ionic Liquid Crystals

    Science.gov (United States)

    Axenov, Kirill V.; Laschat, Sabine

    2011-01-01

    The last five years’ achievements in the synthesis and investigation of thermotropic ionic liquid crystals are reviewed. The present review describes the mesomorphic properties displayed by organic, as well as metal-containing ionic mesogens. In addition, a short overview on the ionic polymer and self-assembled liquid crystals is given. Potential and actual applications of ionic mesogens are also discussed. PMID:28879986

  17. Thermotropic Ionic Liquid Crystals.

    Science.gov (United States)

    Axenov, Kirill V; Laschat, Sabine

    2011-01-14

    The last five years' achievements in the synthesis and investigation of thermotropic ionic liquid crystals are reviewed. The present review describes the mesomorphic properties displayed by organic, as well as metal-containing ionic mesogens. In addition, a short overview on the ionic polymer and self-assembled liquid crystals is given. Potential and actual applications of ionic mesogens are also discussed.

  18. Thermotropic Ionic Liquid Crystals

    OpenAIRE

    Axenov, Kirill V.; Laschat, Sabine

    2011-01-01

    The last five years’ achievements in the synthesis and investigation of thermotropic ionic liquid crystals are reviewed. The present review describes the mesomorphic properties displayed by organic, as well as metal-containing ionic mesogens. In addition, a short overview on the ionic polymer and self-assembled liquid crystals is given. Potential and actual applications of ionic mesogens are also discussed.

  19. Photonic crystal fibers

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper; Hansen, K P; Nielsen, M D

    2003-01-01

    Photonic crystal fibers having a complex microstructure in the transverse plane constitute a new and promising class of optical fibers. Such fibers can either guide light through total internal reflection or the photonic bandgap effect, In this paper, we review the different types and applications...... of photonic crystal fibers with particular emphasis on recent advances in the field....

  20. Tactical Miniature Crystal Oscillator.

    Science.gov (United States)

    1980-08-01

    manufactured by this process are expected to require 30 days to achieve minimum aging rates. (4) FUNDEMENTAL CRYSTAL RETRACE MEASUREMENT. An important crystal...considerable measurement time to detect differences and characterize components. Before investing considerable time in a candidate reactive element, a

  1. Crystals in the LHC

    CERN Multimedia

    Antonella Del Rosso

    2012-01-01

    Bent crystals can be used to deflect charged particle beams. Their use in high-energy accelerators has been investigated for almost 40 years. Recently, a bent crystal was irradiated for the first time in the HiRadMat facility with an extreme particle flux, which crystals would have to withstand in the LHC. The results were very encouraging and confirmed that this technology could play a major role in increasing the beam collimation performance in future upgrades of the machine.   UA9 bent crystal tested with a laser. Charged particles interacting with a bent crystal can be trapped in channelling states and deflected by the atomic planes of the crystal lattice (see box). The use of bent crystals for beam manipulation in particle accelerators is a concept that has been well-assessed. Over the last three decades, a large number of experimental findings have contributed to furthering our knowledge and improving our ability to control crystal-particle interactions. In modern hadron colliders, su...

  2. Optically Anomalous Crystals

    CERN Document Server

    Shtukenberg, Alexander; Kahr, Bart

    2007-01-01

    Optical anomalies in crystals are puzzles that collectively constituted the greatest unsolved problems in crystallography in the 19th Century. The most common anomaly is a discrepancy between a crystal’s symmetry as determined by its shape or by X-ray analysis, and that determined by monitoring the polarization state of traversing light. These discrepancies were perceived as a great impediment to the development of the sciences of crystals on the basis of Curie’s Symmetry Principle, the grand organizing idea in the physical sciences to emerge in the latter half of the 19th Century. Optically Anomalous Crystals begins with an historical introduction covering the contributions of Brewster, Biot, Mallard, Brauns, Tamman, and many other distinguished crystallographers. From this follows a tutorial in crystal optics. Further chapters discuss the two main mechanisms of optical dissymmetry: 1. the piezo-optic effect, and 2. the kinetic ordering of atoms. The text then tackles complex, inhomogeneous crystals, and...

  3. Progress on photonic crystals

    CERN Document Server

    Lecoq, P; Gundacker, S; Hillemanns, H; Jarron, P; Knapitsch, A; Leclercq, J L; Letartre, X; Meyer, T; Pauwels, K; Powolny, F; Seassal, C

    2010-01-01

    The renewal of interest for Time of Flight Positron Emission Tomography (TOF PET) has highlighted the need for increasing the light output of scintillating crystals and in particular for improving the light extraction from materials with a high index of refraction. One possible solution to overcome the problem of total internal reflection and light losses resulting from multiple bouncing within the crystal is to improve the light extraction efficiency at the crystal/photodetector interface by means of photonic crystals, i.e. media with a periodic modulation of the dielectric constant at the wavelength scale. After a short reminder of the underlying principles this contribution proposes to present the very encouraging results we have recently obtained on LYSO pixels and the perspectives on other crystals such as BGO, LuYAP and LuAG. These results confirm the impressive predictions from our previously published Monte Carlo simulations. A detailed description of the sample preparation procedure is given as well ...

  4. Organic semiconductor crystals.

    Science.gov (United States)

    Wang, Chengliang; Dong, Huanli; Jiang, Lang; Hu, Wenping

    2018-01-22

    Organic semiconductors have attracted a lot of attention since the discovery of highly doped conductive polymers, due to the potential application in field-effect transistors (OFETs), light-emitting diodes (OLEDs) and photovoltaic cells (OPVs). Single crystals of organic semiconductors are particularly intriguing because they are free of grain boundaries and have long-range periodic order as well as minimal traps and defects. Hence, organic semiconductor crystals provide a powerful tool for revealing the intrinsic properties, examining the structure-property relationships, demonstrating the important factors for high performance devices and uncovering fundamental physics in organic semiconductors. This review provides a comprehensive overview of the molecular packing, morphology and charge transport features of organic semiconductor crystals, the control of crystallization for achieving high quality crystals and the device physics in the three main applications. We hope that this comprehensive summary can give a clear picture of the state-of-art status and guide future work in this area.

  5. DNA Repair Systems

    Indian Academy of Sciences (India)

    DNA molecule which makes it ideal for storage and propagation of genetic information. ... of these errors are broadly referred to as DNA repair. DNA can ... changes occur in the human genome per day. ..... nails, frequent physical and mental.

  6. Synthesis of DNA

    Science.gov (United States)

    Mariella, Jr., Raymond P.

    2008-11-18

    A method of synthesizing a desired double-stranded DNA of a predetermined length and of a predetermined sequence. Preselected sequence segments that will complete the desired double-stranded DNA are determined. Preselected segment sequences of DNA that will be used to complete the desired double-stranded DNA are provided. The preselected segment sequences of DNA are assembled to produce the desired double-stranded DNA.

  7. Radiation damage to DNA constituents

    International Nuclear Information System (INIS)

    Bergene, R.

    1977-01-01

    The molecular changes of the DNA molecule, in various systems exposed to inoizing radiation, have been the subject of a great number of studies. In the present work electron spin resonance spectroscopy (ESR) has been applied to irradiated crystalline systems, in particular single crystals of DNA subunits and their derivatives. The main conclusions about the molecular damage are based on this technique in combination with molecular orbital calculations. It should be emphasized that the ESR technique is restricted to damage containing unpaired electrons. These unstable intermediates called free radicals seem, however, to be involved in all molecular models describing the action of radiation on DNA. One of the premises for a detailed theory of the radiation induced reactions at the physico-chemical level seems to involve exact knowledge of the induced free radicals as well as the modes of their formation and fate. For DNA, as such, it is hardly possible to arrive at such a level of knowledge since the molecular complexity prevents selective studies of the many different radiation induced products. One possible approach is to study the free radicals formed in the constituents of DNA. In the present work three lines of approach should be mentioned. The first is based on the observation that radical formation in general causes only minor structural alterations to the molecule in question. The use of isotopes with different spin and magnetic moment (in particular deuterium) may also serve a source of information. Deuteration leads to a number of protons, mainly NH - and OH, becoming substituted, and if any of these are involved in interactions with unpaired protons the resonance pattern is influeneed. The third source of information is molecular orbital calculation. The electron spin density distribution is a function in the three dimensional space based on the system's electronic wave functions. This constitutes the basis for the idea that ESR data can be correlated with

  8. Structure of a stacked anthraquinone–DNA complex

    Science.gov (United States)

    De Luchi, Daniela; Usón, Isabel; Wright, Glenford; Gouyette, Catherine; Subirana, Juan A.

    2010-01-01

    The crystal structure of the telomeric sequence d(UBrAGG) interacting with an anthraquinone derivative has been solved by MAD. In all previously studied complexes of intercalating drugs, the drug is usually sandwiched between two DNA base pairs. Instead, the present structure looks like a crystal of stacked anthraquinone molecules in which isolated base pairs are intercalated. Unusual base pairs are present in the structure, such as G·G and A·UBr reverse Watson–Crick base pairs. PMID:20823516

  9. Equilibrium Kinetics Studies and Crystallization Aboard the International Space Station (ISS) Using the Protein Crystallization Apparatus for Microgravity (PCAM)

    Science.gov (United States)

    Achari, Aniruddha; Roeber, Dana F.; Barnes, Cindy L.; Kundrot, Craig E.; Stinson, Thomas N. (Technical Monitor)

    2002-01-01

    Protein Crystallization Apparatus in Microgravity (PCAM) trays have been used in Shuttle missions to crystallize proteins in a microgravity environment. The crystallization experiments are 'sitting drops' similar to that in Cryschem trays, but the reservoir solution is soaked in a wick. From early 2001, crystallization experiments are conducted on the International Space Station using mission durations of months rather than two weeks on previous shuttle missions. Experiments were set up in April 2001 on Flight 6A to characterize the time crystallization experiments will take to reach equilibrium in a microgravity environment using salts, polyethylene glycols and an organic solvent as precipitants. The experiments were set up to gather data for a series of days of activation with different droplet volumes and precipitants. The experimental set up on ISS and results of this study will be presented. These results will help future users of PCAM to choose precipitants to optimize crystallization conditions for their target macromolecules for a particular mission with known mission duration. Changes in crystal morphology and size between the ground and space grown crystals of a protein and a protein -DNA complex flown on the same mission will also be presented.

  10. Disorder in Protein Crystals.

    Science.gov (United States)

    Clarage, James Braun, II

    1990-01-01

    Methods have been developed for analyzing the diffuse x-ray scattering in the halos about a crystal's Bragg reflections as a means of determining correlations in atomic displacements in protein crystals. The diffuse intensity distribution for rhombohedral insulin, tetragonal lysozyme, and triclinic lysozyme crystals was best simulated in terms of exponential displacement correlation functions. About 90% of the disorder can be accounted for by internal movements correlated with a decay distance of about 6A; the remaining 10% corresponds to intermolecular movements that decay in a distance the order of size of the protein molecule. The results demonstrate that protein crystals fit into neither the Einstein nor the Debye paradigms for thermally fluctuating crystalline solids. Unlike the Einstein model, there are correlations in the atomic displacements, but these correlations decay more steeply with distance than predicted by the Debye-Waller model for an elastic solid. The observed displacement correlations are liquid -like in the sense that they decay exponentially with the distance between atoms, just as positional correlations in a liquid. This liquid-like disorder is similar to the disorder observed in 2-D crystals of polystyrene latex spheres, and similar systems where repulsive interactions dominate; hence, these colloidal crystals appear to provide a better analogy for the dynamics of protein crystals than perfectly elastic lattices.

  11. Photonic Crystal Sensors Based on Porous Silicon

    Directory of Open Access Journals (Sweden)

    Claudia Pacholski

    2013-04-01

    Full Text Available Porous silicon has been established as an excellent sensing platform for the optical detection of hazardous chemicals and biomolecular interactions such as DNA hybridization, antigen/antibody binding, and enzymatic reactions. Its porous nature provides a high surface area within a small volume, which can be easily controlled by changing the pore sizes. As the porosity and consequently the refractive index of an etched porous silicon layer depends on the electrochemial etching conditions photonic crystals composed of multilayered porous silicon films with well-resolved and narrow optical reflectivity features can easily be obtained. The prominent optical response of the photonic crystal decreases the detection limit and therefore increases the sensitivity of porous silicon sensors in comparison to sensors utilizing Fabry-Pérot based optical transduction. Development of porous silicon photonic crystal sensors which allow for the detection of analytes by the naked eye using a simple color change or the fabrication of stacked porous silicon photonic crystals showing two distinct optical features which can be utilized for the discrimination of analytes emphasize its high application potential.

  12. Photonic Crystal Sensors Based on Porous Silicon

    Science.gov (United States)

    Pacholski, Claudia

    2013-01-01

    Porous silicon has been established as an excellent sensing platform for the optical detection of hazardous chemicals and biomolecular interactions such as DNA hybridization, antigen/antibody binding, and enzymatic reactions. Its porous nature provides a high surface area within a small volume, which can be easily controlled by changing the pore sizes. As the porosity and consequently the refractive index of an etched porous silicon layer depends on the electrochemial etching conditions photonic crystals composed of multilayered porous silicon films with well-resolved and narrow optical reflectivity features can easily be obtained. The prominent optical response of the photonic crystal decreases the detection limit and therefore increases the sensitivity of porous silicon sensors in comparison to sensors utilizing Fabry-Pérot based optical transduction. Development of porous silicon photonic crystal sensors which allow for the detection of analytes by the naked eye using a simple color change or the fabrication of stacked porous silicon photonic crystals showing two distinct optical features which can be utilized for the discrimination of analytes emphasize its high application potential. PMID:23571671

  13. Crystals in light.

    Science.gov (United States)

    Kahr, Bart; Freudenthal, John; Gunn, Erica

    2010-05-18

    We have made images of crystals illuminated with polarized light for almost two decades. Early on, we abandoned photosensitive chemicals in favor of digital electrophotometry with all of the attendant advantages of quantitative intensity data. Accurate intensities are a boon because they can be used to analytically discriminate small effects in the presence of larger ones. The change in the form of our data followed camera technology that transformed picture taking the world over. Ironically, exposures in early photographs were presumed to correlate simply with light intensity, raising the hope that photography would replace sensorial interpretation with mechanical objectivity and supplant the art of visual photometry. This was only true in part. Quantitative imaging accurate enough to render the separation of crystalloptical quantities had to await the invention of the solid-state camera. Many pioneers in crystal optics were also major figures in the early history of photography. We draw out the union of optical crystallography and photography because the tree that connects the inventors of photography is a structure unmatched for organizing our work during the past 20 years, not to mention that silver halide crystallites used in chemical photography are among the most consequential "crystals in light", underscoring our title. We emphasize crystals that have acquired optical properties such as linear birefringence, linear dichroism, circular birefringence, and circular dichroism, during growth from solution. Other crystalloptical effects were discovered that are unique to curiously dissymmetric crystals containing embedded oscillators. In the aggregate, dyed crystals constitute a generalization of single crystal matrix isolation. Simple crystals provided kinetic stability to include guests such as proteins or molecules in excited states. Molecular lifetimes were extended for the preparation of laser gain media and for the study of the photodynamics of single

  14. Magnetic ions in crystals

    CERN Document Server

    Stevens, K W

    2014-01-01

    There have been many demonstrations, particularly for magnetic impurity ions in crystals, that spin-Hamiltonians are able to account for a wide range of experimental results in terms of much smaller numbers of parameters. Yet they were originally derived from crystal field theory, which contains a logical flaw; electrons on the magnetic ions are distinguished from those on the ligands. Thus there is a challenge: to replace crystal field theory with one of equal or greater predictive power that is based on a surer footing. The theory developed in this book begins with a generic Hamiltonian, on

  15. Silumins alloy crystallization

    Directory of Open Access Journals (Sweden)

    S. Pietrowski

    2009-07-01

    Full Text Available This paper presents the results of research, by ATD method, of hypo-, near- and hyperutectic silumins crystallization containing the following alloying additives: Mg, Ni, Cu, Cr, Mo, W, V. It has been shown that, depending on their concentration may crystallize pre-eutectic or eutectic multicomponent phases containing these alloy additives. It has been revealed that any subsequent crystallizable phase nucleate and grows near the liquid/former crystallized phase interface. In multiphases compound also falls the silicon, resulting in a reduction in its quantity and the fragmentation in the eutectic mixture. As a result, it gets a high hardness of silumins in terms of 110-220HB.

  16. Hypersonic phononic crystals.

    Science.gov (United States)

    Gorishnyy, T; Ullal, C K; Maldovan, M; Fytas, G; Thomas, E L

    2005-03-25

    In this Letter we propose the use of hypersonic phononic crystals to control the emission and propagation of high frequency phonons. We report the fabrication of high quality, single crystalline hypersonic crystals using interference lithography and show that direct measurement of their phononic band structure is possible with Brillouin light scattering. Numerical calculations are employed to explain the nature of the observed propagation modes. This work lays the foundation for experimental studies of hypersonic crystals and, more generally, phonon-dependent processes in nanostructures.

  17. Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding.

    Science.gov (United States)

    Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin; Kurepina, Natalia; Luan, Gan; Oppegard, Lisa M; Hiasa, Hiroshi; Marks, Kevin R; Kerns, Robert J; Berger, James M; Drlica, Karl

    2014-05-02

    DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys(466) gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly(81) and GyrB-Glu(466) residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases.

  18. Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.

    Science.gov (United States)

    Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M; Högberg, Björn

    2013-07-01

    Single-stranded oligonucleotides are important as research tools, as diagnostic probes, in gene therapy and in DNA nanotechnology. Oligonucleotides are typically produced via solid-phase synthesis, using polymer chemistries that are limited relative to what biological systems produce. The number of errors in synthetic DNA increases with oligonucleotide length, and the resulting diversity of sequences can be a problem. Here we present the 'monoclonal stoichiometric' (MOSIC) method for enzyme-mediated production of DNA oligonucleotides. We amplified oligonucleotides from clonal templates derived from single bacterial colonies and then digested cutter hairpins in the products, which released pools of oligonucleotides with precisely controlled relative stoichiometric ratios. We prepared 14-378-nucleotide MOSIC oligonucleotides either by in vitro rolling-circle amplification or by amplification of phagemid DNA in Escherichia coli. Analyses of the formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides.

  19. Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.

    Science.gov (United States)

    Le Bihan, Yann-Vaï; Matot, Béatrice; Pietrement, Olivier; Giraud-Panis, Marie-Josèphe; Gasparini, Sylvaine; Le Cam, Eric; Gilson, Eric; Sclavi, Bianca; Miron, Simona; Le Du, Marie-Hélène

    2013-03-01

    Repressor activator protein 1 (Rap1) is an essential factor involved in transcription and telomere stability in the budding yeast Saccharomyces cerevisiae. Its interaction with DNA causes hypersensitivity to potassium permanganate, suggesting local DNA melting and/or distortion. In this study, various Rap1-DNA crystal forms were obtained using specifically designed crystal screens. Analysis of the DNA conformation showed that its distortion was not sufficient to explain the permanganate reactivity. However, anomalous data collected at the Mn edge using a Rap1-DNA crystal soaked in potassium permanganate solution indicated that the DNA conformation in the crystal was compatible with interaction with permanganate ions. Sequence-conservation analysis revealed that double-Myb-containing Rap1 proteins all carry a fully conserved Arg580 at a position that may favour interaction with permanganate ions, although it is not involved in the hypersensitive cytosine distortion. Permanganate reactivity assays with wild-type Rap1 and the Rap1[R580A] mutant demonstrated that Arg580 is essential for hypersensitivity. AFM experiments showed that wild-type Rap1 and the Rap1[R580A] mutant interact with DNA over 16 successive binding sites, leading to local DNA stiffening but not to accumulation of the observed local distortion. Therefore, Rap1 may cause permanganate hypersensitivity of DNA by forming a pocket between the reactive cytosine and Arg580, driving the permanganate ion towards the C5-C6 bond of the cytosine.

  20. Crystal Genetics, Inc.

    Science.gov (United States)

    Kermani, Bahram G

    2016-07-01

    Crystal Genetics, Inc. is an early-stage genetic test company, focused on achieving the highest possible clinical-grade accuracy and comprehensiveness for detecting germline (e.g., in hereditary cancer) and somatic (e.g., in early cancer detection) mutations. Crystal's mission is to significantly improve the health status of the population, by providing high accuracy, comprehensive, flexible and affordable genetic tests, primarily in cancer. Crystal's philosophy is that when it comes to detecting mutations that are strongly correlated with life-threatening diseases, the detection accuracy of every single mutation counts: a single false-positive error could cause severe anxiety for the patient. And, more importantly, a single false-negative error could potentially cost the patient's life. Crystal's objective is to eliminate both of these error types.

  1. Diffusion in Coulomb crystals.

    Science.gov (United States)

    Hughto, J; Schneider, A S; Horowitz, C J; Berry, D K

    2011-07-01

    Diffusion in Coulomb crystals can be important for the structure of neutron star crusts. We determine diffusion constants D from molecular dynamics simulations. We find that D for Coulomb crystals with relatively soft-core 1/r interactions may be larger than D for Lennard-Jones or other solids with harder-core interactions. Diffusion, for simulations of nearly perfect body-centered-cubic lattices, involves the exchange of ions in ringlike configurations. Here ions "hop" in unison without the formation of long lived vacancies. Diffusion, for imperfect crystals, involves the motion of defects. Finally, we find that diffusion, for an amorphous system rapidly quenched from Coulomb parameter Γ=175 to Coulomb parameters up to Γ=1750, is fast enough that the system starts to crystalize during long simulation runs. These results strongly suggest that Coulomb solids in cold white dwarf stars, and the crust of neutron stars, will be crystalline and not amorphous.

  2. Bipolarons in nonmetallic crystals

    International Nuclear Information System (INIS)

    Vinetskii, V.L.; Pashitskii, E.A.; Yanchuk, V.A.

    1987-01-01

    The binding energy of a bipolaron in an ionic crystal increases substantially in the case of strong anisotropy of the effective masses of the free carriers of the easy plane type or easy axis type. In the second case the polaron is cigar-like in shape and the coaxial configuration of bipolarons is energetically favorable. In this case a significant gain in the binding energy and in the width of the region of existence of the bipolaron, with respect to the dielectric constant and the magnitude of the electron-phonon interaction constant, compared with an isotropic crystal, is obtained only for quasi-two-dimensional, or layered, and quasi-one-dimensional, or chainlike, crystals. This work shows that a significant gain in the binding energy can be obtained by taking into account the anisotropy of the dielectric constant of the crystal and localization of the electron wave functions in directions perpendicular to the layers and chains of atoms

  3. Liquid Crystal Colloids

    Science.gov (United States)

    Smalyukh, Ivan I.

    2018-03-01

    Colloids are abundant in nature, science, and technology, with examples ranging from milk to quantum dots and the colloidal atom paradigm. Similarly, liquid crystal ordering is important in contexts ranging from biological membranes to laboratory models of cosmic strings and liquid crystal displays in consumer devices. Some of the most exciting recent developments in both of these soft matter fields emerge at their interface, in the fast-growing research arena of liquid crystal colloids. Mesoscale self-assembly in such systems may lead to artificial materials and to structures with emergent physical behavior arising from patterning of molecular order and nano- or microparticles into precisely controlled configurations. Liquid crystal colloids show exceptional promise for new discovery that may impinge on composite material fabrication, low-dimensional topology, photonics, and so on. Starting from physical underpinnings, I review the state of the art in this fast-growing field, with a focus on its scientific and technological potential.

  4. Creep of crystals

    International Nuclear Information System (INIS)

    Poirier, J.-P.

    1988-01-01

    Creep mechanisms for metals, ceramics and rocks, effect of pressure and temperature on deformation processes are considered. The role of crystal defects is analysed, different models of creep are described. Deformation mechanisms maps for different materials are presented

  5. Synthesis, characterization, crystal structure and DNA-binding study ...

    Indian Academy of Sciences (India)

    BOLIN

    xxxx Mobile: xxxx. *For Correspondence .... Casida M E 1996 In Recent developments and Applications of Modern density functional theoryJ M ... Thesis. Author name, Year, Title of thesis, (University name, city, country) page number ...

  6. Thermotropic Ionic Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Sabine Laschat

    2011-01-01

    Full Text Available The last five years’ achievements in the synthesis and investigation of thermotropic ionic liquid crystals are reviewed. The present review describes the mesomorphic properties displayed by organic, as well as metal-containing ionic mesogens. In addition, a short overview on the ionic polymer and self-assembled liquid crystals is given. Potential and actual applications of ionic mesogens are also discussed.

  7. Building a crystal palace

    CERN Multimedia

    2007-01-01

    The end-caps of the CMS electromagnetic calorimeter (ECAL) take shape as the first quadrant was completed on Wednesday 3 October. 1831 crystals, organised into five by five blocks named ‘supercrystals’, make up the first quadrant of Dee 1.With the 61,200-crystal barrel of its electromagnetic calorimeter (ECAL) complete, CMS is now building the endcaps, on the tenth anniversary of their initial design. Crystals for the endcaps were the last to be made, so the race is now on to have them all in place and ready for the turn-on of the LHC next year. Assembly of the first of eight quadrants began in June and crystal mounting was completed on Wednesday 3 October. Each crystal is transparent, has a volume just larger than a CERN coffee cup yet weighs a huge 1.5kg. 1831 of these lead tungstate crystals went into the first quadrant from a total 14,648 in the endcaps. The lead and tungsten account for 86% of each crystal’s weight, but as project leader Dave Cockerill expl...

  8. Two high-mobility group box domains act together to underwind and kink DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Giraldo, R.; Acosta-Reyes, F. J. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Malarkey, C. S. [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Saperas, N. [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain); Churchill, M. E. A., E-mail: mair.churchill@ucdenver.edu [University of Colorado School of Medicine, Aurora, CO 80045 (United States); Campos, J. L., E-mail: mair.churchill@ucdenver.edu [Universitat Politecnica de Catalunya, 08028 Barcelona (Spain)

    2015-06-30

    The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.

  9. Two high-mobility group box domains act together to underwind and kink DNA

    International Nuclear Information System (INIS)

    Sánchez-Giraldo, R.; Acosta-Reyes, F. J.; Malarkey, C. S.; Saperas, N.; Churchill, M. E. A.; Campos, J. L.

    2015-01-01

    The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA

  10. Synthesis and binding affinity analysis of α1-2- and α1-6-O/S-linked dimannosides for the elucidation of sulfur in glycosidic bonds using quartz crystal microbalance sensors

    DEFF Research Database (Denmark)

    Norberg, Oscar; Wu, Bin; Thota, Niranjan

    2017-01-01

    with the cognate lectin concanavalin A. Mannose-presenting QCM sensors were produced using photoinitiated, nitrene-mediated immobilization methods, and the subsequent binding study was performed in an automated flow-through instrumentation, and correlated with data from isothermal titration calorimetry...

  11. DNA responds to ionizing radiation as an insulator, not as a "molecular wire"

    NARCIS (Netherlands)

    Debije, M.G.; Milano, M.T.; Bernhard, W.A.

    1999-01-01

    The yields of radicals trapped on DNA, measured by EPR spectroscopy of oligodeoxyribonucleotide crystals (the EPR spectrum of a single crystal of d(CCCTAGGG) is shown), are found to be very high (0.7 µmol¿J-1) and insensitive to long-range (>106 base pairs) versus short-range stacking (8 base pairs)

  12. DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme

    NARCIS (Netherlands)

    Zaremba, M.; Lyubchenko, Y.L.; Laurens, N.; van den Broek, B.; Wuite, G.J.L.; Siksnys, V.

    2010-01-01

    To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or

  13. Tertiary Structures of the Escherichia coli and Human Chromosome 21 Molecules of DNA

    Czech Academy of Sciences Publication Activity Database

    Hanzálek, Petr; Kypr, Jaroslav

    2001-01-01

    Roč. 283, č. 1 (2001), s. 219-223 ISSN 0006-291X R&D Projects: GA AV ČR IAA5004802 Institutional research plan: CEZ:AV0Z5004920 Keywords : DNA crystal structures * phosphorus atom representation * genomic DNA molecules Subject RIV: BO - Biophysics Impact factor: 2.946, year: 2001

  14. Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation.

    Science.gov (United States)

    Ngo, Huu B; Lovely, Geoffrey A; Phillips, Rob; Chan, David C

    2014-01-01

    TFAM (transcription factor A, mitochondrial) is a DNA-binding protein that activates transcription at the two major promoters of mitochondrial DNA (mtDNA)--the light strand promoter (LSP) and the heavy strand promoter 1 (HSP1). Equally important, it coats and packages the mitochondrial genome. TFAM has been shown to impose a U-turn on LSP DNA; however, whether this distortion is relevant at other sites is unknown. Here we present crystal structures of TFAM bound to HSP1 and to nonspecific DNA. In both, TFAM similarly distorts the DNA into a U-turn. Yet, TFAM binds to HSP1 in the opposite orientation from LSP explaining why transcription from LSP requires DNA bending, whereas transcription at HSP1 does not. Moreover, the crystal structures reveal dimerization of DNA-bound TFAM. This dimerization is dispensable for DNA bending and transcriptional activation but is important in DNA compaction. We propose that TFAM dimerization enhances mitochondrial DNA compaction by promoting looping of the DNA.

  15. DNA preservation in silk.

    Science.gov (United States)

    Liu, Yawen; Zheng, Zhaozhu; Gong, He; Liu, Meng; Guo, Shaozhe; Li, Gang; Wang, Xiaoqin; Kaplan, David L

    2017-06-27

    The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility. After air-drying and water extraction, 50-70% of the DNA and silk could be retrieved and showed a single band on electrophoretic gels. 6% silk/DNA + PT-filter samples provided improved stability in comparison with 3% silk/DNA + filter samples and DNA + filter samples for DNA preservation, with ∼40% of the band intensity remaining at 37 °C after 40 days and ∼10% after exposure to UV light for 10 hours. Quantitative analysis using the PicoGreen assay confirmed the results. The use of Tris/borate/EDTA (TBE) buffer enhanced the preservation and/or extraction of the DNA. The DNA extracted after storage maintained integrity and function based on serving as a functional template for PCR amplification of the gene for zinc finger protein 750 (ZNF750) and for transgene expression of red fluorescence protein (dsRed) in HEK293 cells. The high molecular weight and high content of a crystalline beta-sheet structure formed on the coated surfaces likely accounted for the preservation effects observed for the silk/DNA + PT-filter samples. Although similar preservation effects were also obtained for lyophilized silk/DNA samples, the rapid and simple processing available with the silk-DNA-filter membrane system makes it appealing for future applications.

  16. Force induced DNA melting

    International Nuclear Information System (INIS)

    Santosh, Mogurampelly; Maiti, Prabal K

    2009-01-01

    When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates by roughly twice its initial contour length at a pulling force of about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying a force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA, this being a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double-strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA starts melting abruptly/smoothly above a critical force depending on the pulling direction. The critical force f m , at which DNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base pairs. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.

  17. DNA damage and autophagy

    International Nuclear Information System (INIS)

    Rodriguez-Rocha, Humberto; Garcia-Garcia, Aracely; Panayiotidis, Mihalis I.; Franco, Rodrigo

    2011-01-01

    Both exogenous and endogenous agents are a threat to DNA integrity. Exogenous environmental agents such as ultraviolet (UV) and ionizing radiation, genotoxic chemicals and endogenous byproducts of metabolism including reactive oxygen species can cause alterations in DNA structure (DNA damage). Unrepaired DNA damage has been linked to a variety of human disorders including cancer and neurodegenerative disease. Thus, efficient mechanisms to detect DNA lesions, signal their presence and promote their repair have been evolved in cells. If DNA is effectively repaired, DNA damage response is inactivated and normal cell functioning resumes. In contrast, when DNA lesions cannot be removed, chronic DNA damage triggers specific cell responses such as cell death and senescence. Recently, DNA damage has been shown to induce autophagy, a cellular catabolic process that maintains a balance between synthesis, degradation, and recycling of cellular components. But the exact mechanisms by which DNA damage triggers autophagy are unclear. More importantly, the role of autophagy in the DNA damage response and cellular fate is unknown. In this review we analyze evidence that supports a role for autophagy as an integral part of the DNA damage response.

  18. Time crystals: a review

    Science.gov (United States)

    Sacha, Krzysztof; Zakrzewski, Jakub

    2018-01-01

    Time crystals are time-periodic self-organized structures postulated by Frank Wilczek in 2012. While the original concept was strongly criticized, it stimulated at the same time an intensive research leading to propositions and experimental verifications of discrete (or Floquet) time crystals—the structures that appear in the time domain due to spontaneous breaking of discrete time translation symmetry. The struggle to observe discrete time crystals is reviewed here together with propositions that generalize this concept introducing condensed matter like physics in the time domain. We shall also revisit the original Wilczek’s idea and review strategies aimed at spontaneous breaking of continuous time translation symmetry.

  19. Thermodynamics of Crystals

    Science.gov (United States)

    Navrotsky, Alexandra

    Thermodynamics of Crystals is a gold mine of a references bargain with more derivations of useful equations per dollar, or per page, than almost any other book I know. Useful to whom? To the solid state physicist, the solid state chemist working the geophysicist, the rock mechanic, the mineral physicist. Useful for what? For lattice dynamics, crystal potentials, band structure. For elegant, rigorous, and concise derivations of fundamental equations. For comparison of levels of approximation. For some data and physical insights, especially for metals and simple halides. This book is a reissue, with some changes and additions, of a 1970 treatise. It ages well, since the fundamentals do not change.

  20. Photonic Crystal Fibres

    DEFF Research Database (Denmark)

    Bjarklev, Anders Overgaard; Broeng, Jes; Sanchez Bjarklev, Araceli

    Photonic crystal fibres represent one of the most active research areas today in the field of optics. The diversity of applications that may be addressed by these fibres and their fundamental appeal, by opening up the possibility of guiding light in a radically new way compared to conventional...... optical fibres, have spun an interest from almost all areas of optics and photonics. The aim of this book is to provide an understanding of the different types of photonic crystal fibres and to outline some of the many new and exciting applications that these fibres offer. The book is intended for both...

  1. DNA Open states and DNA hydratation

    International Nuclear Information System (INIS)

    Lema-Larre, B. de; Martin-Landrove, M

    1995-01-01

    It is a very well-known fact that an protonic exchange exists among natural DNA filaments and synthetic polynucleotides with the solvent (1--2). The existence of DNA open states, that is to say states for which the interior of the DNA molecule is exposed to the external environment, it has been demonstrated by means of proton-deuterium exchange (3). This work has carried out experiments measuring the dispersion of the traverse relaxation rate (4), as a pulsation rate function in a Carr-Purcell-Meiboom-Gill (CPMG) pulses sequence rate, to determine changes in the moist layer of the DNA molecule. The experiments were carried out under different experimental conditions in order to vary the probability that open states occurs, such as temperature or the exposure to electromagnetic fields. Some theoretical models were supposed to adjust the experimental results including those related to DNA non linear dynamic [es

  2. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

  3. Enzymatic Production of Monoclonal Stoichiometric Single-Stranded DNA Oligonucleotides

    Science.gov (United States)

    Ducani, Cosimo; Kaul, Corinna; Moche, Martin; Shih, William M.; Högberg, Björn

    2013-01-01

    Single-stranded oligonucleotides are important as research tools as probes for diagnostics and gene therapy. Today, production of oligonucleotides is done via solid-phase synthesis. However, the capabilities of current polymer chemistry are limited in comparison to what can be produced in biological systems. The errors in synthetic DNA increases with oligonucleotide length, and sequence diversity can often be a problem. Here, we present the Monoclonal Stoichiometric (MOSIC) method for enzymatic DNA oligonucleotide production. Using this method, we amplify oligonucleotides from clonal templates followed by digestion of a cutter-hairpin, resulting in pools of monoclonal oligonucleotides with precisely controlled relative stoichiometric ratios. We present data where MOSIC oligonucleotides, 14–378 nt long, were prepared either by in vitro rolling-circle amplification, or by amplification in Escherichia coli in the form of phagemid DNA. The formation of a DNA crystal and folding of DNA nanostructures confirmed the scalability, purity and stoichiometry of the produced oligonucleotides. PMID:23727986

  4. Immunoassay of DNA damage

    International Nuclear Information System (INIS)

    Gasparro, F.P.; Santella, R.M.

    1988-01-01

    The direct photomodification of DNA by ultraviolet light or the photo-induced addition of exogenous compounds to DNA components results in alterations of DNA structure ranging from subtle to profound. There are two consequences of these conformational changes. First, cells in which the DNA has been damaged are capable of executing repair steps. Second, the DNA which is usually of very low immunogenicity now becomes highly antigenic. This latter property has allowed the production of a series of monoclonal antibodies that recognize photo-induced DNA damage. Monoclonal antibodies have been generated that recognize the 4',5'-monoadduct and the crosslink of 8-methoxypsoralen in DNA. In addition, another antibody has been prepared which recognizes the furan-side monoadduct of 6,4,4'-trimethylangelicin in DNA. These monoclonal antibodies have been characterized as to sensitivity and specificity using non-competitive and competitive enzyme-linked-immunosorbent assays (ELISA). (author)

  5. Immunoassay of DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Gasparro, F P; Santella, R M

    1988-09-01

    The direct photomodification of DNA by ultraviolet light or the photo-induced addition of exogenous compounds to DNA components results in alterations of DNA structure ranging from subtle to profound. There are two consequences of these conformational changes. First, cells in which the DNA has been damaged are capable of executing repair steps. Second, the DNA which is usually of very low immunogenicity now becomes highly antigenic. This latter property has allowed the production of a series of monoclonal antibodies that recognize photo-induced DNA damage. Monoclonal antibodies have been generated that recognize the 4',5'-monoadduct and the crosslink of 8-methoxypsoralen in DNA. In addition, another antibody has been prepared which recognizes the furan-side monoadduct of 6,4,4'-trimethylangelicin in DNA. These monoclonal antibodies have been characterized as to sensitivity and specificity using non-competitive and competitive enzyme-linked-immunosorbent assays (ELISA).

  6. DNA computing models

    CERN Document Server

    Ignatova, Zoya; Zimmermann, Karl-Heinz

    2008-01-01

    In this excellent text, the reader is given a comprehensive introduction to the field of DNA computing. The book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines.

  7. DNA tagged microparticles

    Science.gov (United States)

    Farquar, George Roy; Leif, Roald N; Wheeler, Elizabeth

    2015-05-05

    A simulant that includes a carrier and DNA encapsulated in the carrier. Also a method of making a simulant including the steps of providing a carrier and encapsulating DNA in the carrier to produce the simulant.

  8. Modeling DNA Replication.

    Science.gov (United States)

    Bennett, Joan

    1998-01-01

    Recommends the use of a model of DNA made out of Velcro to help students visualize the steps of DNA replication. Includes a materials list, construction directions, and details of the demonstration using the model parts. (DDR)

  9. Crystallization and preliminary X-ray analysis of the RAD protein from Antirrhinum majus

    International Nuclear Information System (INIS)

    Stevenson, Clare E. M.; Burton, Nicolas; Costa, Manuela; Nath, Utpal; Dixon, Ray A.; Coen, Enrico S.; Lawson, David M.

    2005-01-01

    An 8 kDa proteolytic fragment of the A. majus RADIALIS protein was crystallized and X-ray data were collected to 2 Å resolution. Crystals of the RADIALIS protein from Antirrhinum majus were grown by vapour diffusion after limited proteolysis. Mass spectrometry indicated that an 8 kDa fragment had been crystallized corresponding to the predicted MYB DNA-binding domain. X-ray data collected at room temperature were consistent with tetragonal symmetry, whereas data collected at 100 K using crystals cryoprotected by supplementing the mother liquor with ethylene glycol conformed to orthorhombic symmetry. It was subsequently shown that crystals soaked in cryoprotectants that were ‘osmolality-matched’ to the mother liquor retained tetragonal symmetry. Using these crystals, X-ray data were collected in-house to a maximum resolution of 2 Å

  10. Design and Assembly of DNA Nano-Objects and 2D DNA Origami Arrays

    Science.gov (United States)

    Liu, Wenyan

    DNA, which plays a central role in biology as the carrier of genetic information, is also an excellent candidate for structural nanotechnology. Researches have proven that a variety of complicated DNA assemblies, such as objects, 2D & 3D crystals, and nanomechanical devices, can be fabricated through the combination of robust branched DNA motifs and sticky ends. This dissertation focuses on the design and construction of DNA nano--objects and 2D DNA origami arrays. In this dissertation, we first describe the formation of a triangular species that has four strands per edge, held together by PX interactions. We demonstrate by nondenaturing gel electrophoresis and by atomic force microscopy (AFM) that we can combine a partial triangle with other strands to form a robust four--stranded molecule. By combining them with a novel three--domain molecule, we also demonstrate by AFM that these triangles can be self--assembled into a linear array. Second, we demonstrate our attempts to design and self--assemble 2D DNA origami arrays using several different strategies. Specifically, we introduce the self--assembly of 2D DNA origami lattices using a symmetric cross--like design. This design strategy resulted in a well--ordered woven latticework array with edge dimensions of 2--3 mum. This size is likely to be large enough to connect bottom-up methods of patterning with top--down approaches. Third, we illustrate the design and construction of DNA nano--objects for exploring the substrate preferences of topoisomerase (topo) II. We designed and fabricated four double rhombus--like DNA molecules, each of which contains a different conformation of crossover in the middle, as possible substrates to establish the structural preferences for topo II. We characterized the formation of each substrate molecule by gel electrophoresis. Finally, we study the effect of M13 DNA knotting on the formation of the DNA origami tiles. We demonstrate by atomic force microscopy (AFM) that knotted M13

  11. The Crystal Hotel: A Microfluidic Approach to Biomimetic Crystallization.

    Science.gov (United States)

    Gong, Xiuqing; Wang, Yun-Wei; Ihli, Johannes; Kim, Yi-Yeoun; Li, Shunbo; Walshaw, Richard; Chen, Li; Meldrum, Fiona C

    2015-12-02

    A "crystal hotel" microfluidic device that allows crystal growth in confined volumes to be studied in situ is used to produce large calcite single crystals with predefined crystallographic orientation, microstructure, and shape by control of the detailed physical environment, flow, and surface chemistry. This general approach can be extended to form technologically important, nanopatterned single crystals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Analysis of the role of PCNA-DNA contacts during clamp loading

    Directory of Open Access Journals (Sweden)

    Goedken Eric R

    2010-01-01

    Full Text Available Abstract Background Sliding clamps, such as Proliferating Cell Nuclear Antigen (PCNA in eukaryotes, are ring-shaped protein complexes that encircle DNA and enable highly processive DNA replication by serving as docking sites for DNA polymerases. In an ATP-dependent reaction, clamp loader complexes, such as the Replication Factor-C (RFC complex in eukaryotes, open the clamp and load it around primer-template DNA. Results We built a model of RFC bound to PCNA and DNA based on existing crystal structures of clamp loaders. This model suggests that DNA would enter the clamp at an angle during clamp loading, thereby interacting with positively charged residues in the center of PCNA. We show that simultaneous mutation of Lys 20, Lys 77, Arg 80, and Arg 149, which interact with DNA in the RFC-PCNA-DNA model, compromises the ability of yeast PCNA to stimulate the DNA-dependent ATPase activity of RFC when the DNA is long enough to extend through the clamp. Fluorescence anisotropy binding experiments show that the inability of the mutant clamp proteins to stimulate RFC ATPase activity is likely caused by reduction in the affinity of the RFC-PCNA complex for DNA. We obtained several crystal forms of yeast PCNA-DNA complexes, measuring X-ray diffraction data to 3.0 Å resolution for one such complex. The resulting electron density maps show that DNA is bound in a tilted orientation relative to PCNA, but makes different contacts than those implicated in clamp loading. Because of apparent partial disorder in the DNA, we restricted refinement of the DNA to a rigid body model. This result contrasts with previous analysis of a bacterial clamp bound to DNA, where the DNA was well resolved. Conclusion Mutational analysis of PCNA suggests that positively charged residues in the center of the clamp create a binding surface that makes contact with DNA. Disruption of this positive surface, which had not previously been implicated in clamp loading function, reduces RFC

  13. DNA: Structure and function

    DEFF Research Database (Denmark)

    Sinden, Richard R.; E. Pearson, Christopher; N. Potaman, Vladimir

    1998-01-01

    This chapter discusses the structure and function of DNA. DNA occupies a critical role in cells, because it is the source of all intrinsic genetic information. Chemically, DNA is a very stable molecule, a characteristic important for a macromolecule that may have to persist in an intact form...

  14. Replicating animal mitochondrial DNA

    Directory of Open Access Journals (Sweden)

    Emily A. McKinney

    2013-01-01

    Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

  15. Hydrothermally grown zeolite crystals

    International Nuclear Information System (INIS)

    Durrani, S.K.; Qureshi, A.H.; Hussain, M.A.; Qazi, N.K.

    2009-01-01

    The aluminium-deficient and ferrosilicate zeolite-type materials were synthesized by hydrothermal process at 150-170 degree C for various periods of time from the mixtures containing colloidal reactive silica, sodium aluminate, sodium hydroxide, iron nitrate and organic templates. Organic polycation templates were used as zeolite crystal shape modifiers to enhance relative growth rates. The template was almost completely removed from the zeolite specimens by calcination at 550 degree C for 8h in air. Simultaneous thermogravimetric (TG) and differential thermal analysis (DTA) was performed to study the removal of water molecules and the amount of organic template cations occluded inside the crystal pore of zeolite framework. The 12-13% weight loss in the range of (140-560 degree C) was associated with removal of the (C/sub 3/H/sub 7/)/sub 4/ N+ cation and water molecules. X-ray diffraction (XRD) analysis and scanning electron microscope (SEM) techniques were employed to study the structure, morphology and surface features of hydrothermally grown aluminium-deficient and ferrosilicate zeolite-type crystals. In order to elucidate the mode of zeolite crystallization the crystallinity and unit cell parameters of the materials were determined by XRD, which are the function of Al and Fe contents of zeolites. (author)

  16. Poet Lake Crystal Approval

    Science.gov (United States)

    This September 19, 2016 letter from EPA approves the petition from Poet Biorefining-Lake Crystal, regarding non-grandfathered ethanol produced through a dry mill process, qualifying under the Clean Air Act for renewable fuel (D-code 6) RINs under the RFS

  17. Liquid crystal display

    International Nuclear Information System (INIS)

    Takami, K.

    1981-01-01

    An improved liquid crystal display device is described which can display letters, numerals and other necessary patterns in the night time using a minimized amount of radioactive material. To achieve this a self-luminous light source is placed in a limited region corresponding to a specific display area. (U.K.)

  18. Soap Bubbles and Crystals

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 6. Soap Bubbles and Crystals. Jean E Taylor. General Article Volume 11 Issue 6 June 2006 pp 26-30. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/011/06/0026-0030. Keywords. Soap bubble ...

  19. Agile Photonic Crystals

    Science.gov (United States)

    2011-01-03

    75, pp. 3253-3256, Oct. 1995. [24] F. Benabid, J. C. Knight, and P. S. J. Russell, “Particle levitation and guidance in hollow-core photonic crystal...B. Mizaikoff, “Midinfrared sensors meet nanotechnology: Trace gas sensing with quantum cascade lasers inside photonic band-gap hollow waveguides

  20. The Crystal Set

    Science.gov (United States)

    Greenslade, Thomas B., Jr.

    2014-01-01

    In past issues of this journal, the late H. R. Crane wrote a long series of articles under the running title of "How Things Work." In them, Dick dealt with many questions that physics teachers asked themselves, but did not have the time to answer. This article is my attempt to work through the physics of the crystal set, which I thought…

  1. WORKSHOP: Scintillating crystals

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1992-12-15

    Scintillating crystals are one of the big spinoff success stories of particle physics, and from 22-26 September an international workshop in Chamonix in the French Alps looked at the increasing role of these materials in pure and applied science and in industry.

  2. The CMS crystal calorimeter

    CERN Document Server

    Lustermann, W

    2004-01-01

    The measurement of the energy of electrons and photons with very high accuracy is of primary importance far the study of many physics processes at the Large Hadron Collider (LHC), in particular for the search of the Higgs Boson. The CMS experiment will use a crystal calorimeter with pointing geometry, almost covering 4p, as it offers a very good energy resolution. It is divided into a barrel composed of 61200 lead tungstate crystals, two end-caps with 14648 crystals and a pre-shower detector in front of the end-cap. The challenges of the calorimeter design arise from the high radiation environment, the 4 Tesla magnetic eld, the high bunch crossing rate of 40 MHz and the large dynamic range, requiring the development of fast, radiation hard crystals, photo-detectors and readout electronics. An overview of the construction and design of the calorimeter will be presented, with emphasis on some of the details required to meet the demanding performance goals. 19 Refs.

  3. Positrons in ionic crystals

    International Nuclear Information System (INIS)

    Pareja, R.

    1988-01-01

    Positron annihilation experiments in ionic crystals are reviewed and their results are arranged. A discussion about the positron states in these materials is made in the light of these results and the different proposed models. The positronium in alkali halides is specially considered. (Author)

  4. WORKSHOP: Scintillating crystals

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    Scintillating crystals are one of the big spinoff success stories of particle physics, and from 22-26 September an international workshop in Chamonix in the French Alps looked at the increasing role of these materials in pure and applied science and in industry

  5. Thermoelectricity in liquid crystals

    Science.gov (United States)

    Mohd Said, Suhana; Nordin, Abdul Rahman; Abdullah, Norbani; Balamurugan, S.

    2015-09-01

    The thermoelectric effect, also known as the Seebeck effect, describes the conversion of a temperature gradient into electricity. A Figure of Merit (ZT) is used to describe the thermoelectric ability of a material. It is directly dependent on its Seebeck coefficient and electrical conductivity, and inversely dependent on its thermal conductivity. There is usually a compromise between these parameters, which limit the performance of thermoelectric materials. The current achievement for ZT~2.2 falls short of the expected threshold of ZT=3 to allow its viability in commercial applications. In recent times, advances in organic thermoelectrics been significant, improving by over 3 orders of magnitude over a period of about 10 years. Liquid crystals are newly investigated as candidate thermoelectric materials, given their low thermal conductivity, inherent ordering, and in some cases, reasonable electrical conductivity. In this work the thermoelectric behaviour of a discotic liquid crystal, is discussed. The DLC was filled into cells coated with a charge injector, and an alignment of the columnar axis perpendicular to the substrate was allowed to form. This thermoelectric behavior can be correlated to the order-disorder transition. A reasonable thermoelectric power in the liquid crystal temperature regime was noted. In summary, thermoelectric liquid crystals may have the potential to be utilised in flexible devices, as a standalone power source.

  6. Chemistry of microporous crystals

    International Nuclear Information System (INIS)

    Inui, Tomoyuki; Namba, Seitaro; Tatsumi, Takashi

    1991-01-01

    This volume contains three papers which are in INIS scope, entitled respectively: 129 Xe-NMR study of the crystallization of SAPO-37, NMR studies of cation localization in zeolites, developments in x-ray and neutron diffraction methods for zeolites. (H.W.). refs.; figs.; tabs

  7. Electrical properties of molecular crystals

    International Nuclear Information System (INIS)

    Barraud, A.

    1968-01-01

    This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [fr

  8. Fast phylogenetic DNA barcoding

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Boomsma, Wouter Krogh; Willerslev, Eske

    2008-01-01

    We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect...... DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria...... for determining the taxonomic level at which a particular DNA sequence can be assigned....

  9. Radiation and DNA

    Energy Technology Data Exchange (ETDEWEB)

    Riabchenko, N I

    1979-01-01

    Consideration is given to the effects of ionizing radiation on the structure of DNA. Physical and chemical methods of determining radiation damage to the primary (polynucleotide chain and nitrogenous base) and secondary (helical) structure of DNA are discussed, and the effects of ionizing radiation on deoxyribonucleoprotein complexes are considered. The radiolysis of DNA in vitro and in bacterial and mammalian cells is examined and cellular mechanisms for the repair of radiation-damaged DNA are considered, taking into account single-strand and double-strand breaks, gamma-radiation damage and deoxyribonucleoprotein-membrane complex damage. Postradiation DNA degradation in bacteria and lymphatic cells is also discussed.

  10. DNA-Mediated Electrochemistry

    Science.gov (United States)

    Gorodetsky, Alon A.; Buzzeo, Marisa C.

    2009-01-01

    The base pair stack of DNA has been demonstrated as a medium for long range charge transport chemistry both in solution and at DNA-modified surfaces. This chemistry is exquisitely sensitive to structural perturbations in the base pair stack as occur with lesions, single base mismatches, and protein binding. We have exploited this sensitivity for the development of reliable electrochemical assays based on DNA charge transport at self-assembled DNA monolayers. Here we discuss the characteristic features, applications, and advantages of DNA-mediated electrochemistry. PMID:18980370

  11. Optimization of photonic crystal cavities

    DEFF Research Database (Denmark)

    Wang, Fengwen; Sigmund, Ole

    2017-01-01

    We present optimization of photonic crystal cavities. The optimization problem is formulated to maximize the Purcell factor of a photonic crystal cavity. Both topology optimization and air-hole-based shape optimization are utilized for the design process. Numerical results demonstrate...... that the Purcell factor of the photonic crystal cavity can be significantly improved through optimization....

  12. Production of polarizing Heusler crystals

    Energy Technology Data Exchange (ETDEWEB)

    Courtois, P. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

    1999-11-01

    Heusler crystals simultaneously produce monochromatized and polarized neutrons. However, in the past, it was difficult to produce these crystals. In collaboration with the neutron scattering group of CEA Grenoble and LLB Saclay, the production of high quality Heusler crystals has been established at ILL. (author) 3 refs., 2 figs., 1 tab.

  13. DNA fragmentation in spermatozoa

    DEFF Research Database (Denmark)

    Rex, A S; Aagaard, J.; Fedder, J

    2017-01-01

    Sperm DNA Fragmentation has been extensively studied for more than a decade. In the 1940s the uniqueness of the spermatozoa protein complex which stabilizes the DNA was discovered. In the fifties and sixties, the association between unstable chromatin structure and subfertility was investigated....... In the seventies, the impact of induced DNA damage was investigated. In the 1980s the concept of sperm DNA fragmentation as related to infertility was introduced as well as the first DNA fragmentation test: the Sperm Chromatin Structure Assay (SCSA). The terminal deoxynucleotidyl transferase nick end labelling...... (TUNEL) test followed by others was introduced in the nineties. The association between DNA fragmentation in spermatozoa and pregnancy loss has been extensively investigated spurring the need for a therapeutic tool for these patients. This gave rise to an increased interest in the aetiology of DNA damage...

  14. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

  15. Production, purification, crystallization and structure determination of H-1 Parvovirus

    International Nuclear Information System (INIS)

    Halder, Sujata; Nam, Hyun-Joo; Govindasamy, Lakshmanan; Vogel, Michèle; Dinsart, Christiane; Salomé, Nathalie; McKenna, Robert; Agbandje-McKenna, Mavis

    2012-01-01

    The production, purification, crystallization and crystallographic analysis of H-1 Parvovirus, a gene-therapy vector, are reported. Crystals of H-1 Parvovirus (H-1PV), an antitumor gene-delivery vector, were obtained for DNA-containing capsids and diffracted X-rays to 2.7 Å resolution using synchrotron radiation. The crystals belonged to the monoclinic space group P2 1 , with unit-cell parameters a = 255.4, b = 350.4, c = 271.6 Å, β = 90.34°. The unit cell contained two capsids, with one capsid per crystallographic asymmetric unit. The H-1PV structure has been determined by molecular replacement and is currently being refined

  16. Graphene-based photonic crystal

    International Nuclear Information System (INIS)

    Berman, Oleg L.; Boyko, Vladimir S.; Kezerashvili, Roman Ya.; Kolesnikov, Anton A.; Lozovik, Yurii E.

    2010-01-01

    A novel type of photonic crystal formed by embedding a periodic array of constituent stacks of alternating graphene and dielectric discs into a background dielectric medium is proposed. The photonic band structure and transmittance of such photonic crystal are calculated. The graphene-based photonic crystals can be used effectively as the frequency filters and waveguides for the far infrared region of electromagnetic spectrum. Due to substantial suppression of absorption of low-frequency radiation in doped graphene the damping and skin effect in the photonic crystal are also suppressed. The advantages of the graphene-based photonic crystal are discussed.

  17. Liquid crystals in tribology.

    Science.gov (United States)

    Carrión, Francisco-José; Martínez-Nicolás, Ginés; Iglesias, Patricia; Sanes, José; Bermúdez, María-Dolores

    2009-09-18

    Two decades ago, the literature dealing with the possible applications of low molar mass liquid crystals, also called monomer liquid crystals (MLCs), only included about 50 references. Today, thousands of papers, conference reports, books or book chapters and patents refer to the study and applications of MLCs as lubricants and lubricant additives and efforts are made to develop new commercial applications. The development of more efficient lubricants is of paramount technological and economic relevance as it is estimated that half the energy consumption is dissipated as friction. MLCs have shown their ability to form ordered boundary layers with good load-carrying capacity and to lower the friction coefficients, wear rates and contact temperature of sliding surfaces, thus contributing to increase the components service life and to save energy. This review includes the use of MLCs in lubrication, and dispersions of MLCs in conventional polymers (PDMLCs). Finally, new lubricating system composed of MLC blends with surfactants, ionic liquids or nanophases are considered.

  18. Liquid crystal dimers

    CERN Document Server

    Kumar Pal, Santanu

    2017-01-01

    This book covers in-depth discussion of design principles, synthesis and thermal behavior of all types of liquid crystal (LC) dimers. The text presents recent advances in the field of LC dimers consisting of different mesogenic units such as calamitic, discotic and bent-core molecules. It starts with a chapter on the introduction of liquid crystal dimers, including their odd-even behavior, basic classification of dimers and common mesophases in dimers. The text shows how the molecular architectures are being used to develop new materials to study a range of interesting phenomena such as the biaxial nematic phase containing rod-like and disc-like mesogenic units. Finally, the text presents perspectives related to technological relevance of these dimers such as dopants in LC display mixtures exhibiting faster relaxation time, strong flexoelectric coupling and others to effect control over the properties of these materials.

  19. Nonlinear Photonic Crystal Fibers

    DEFF Research Database (Denmark)

    Hansen, Kim Per

    2004-01-01

    Despite the general recession in the global economy and the collapse of the optical telecommunication market, research within specialty fibers is thriving. This is, more than anything else, due to the technology transition from standard all-glass fibers to photonic crystal fibers, which, instead....... The freedom to design the dispersion profile of the fibers is much larger and it is possible to create fibers, which support only a single spatial mode, regardless of wavelength. In comparison, the standard dispersion-shifted fibers are limited by a much lower index-contrast between the core and the cladding...... in 1996, and are today on their way to become the dominating technology within the specialty fiber field. Whether they will replace the standard fiber in the more traditional areas like telecommunication transmission, is not yet clear, but the nonlinear photonic crystal fibers are here to stay....

  20. Liquid crystal colloids

    CERN Document Server

    Muševič, Igor

    2017-01-01

    This book brings together the many concepts and discoveries in liquid crystal colloids contributed over the last twenty years and scattered across numerous articles and book chapters. It provides both a historical overview of the development of the field and a clear perspective on the future applications in photonics. The book covers all phenomena observed in liquid crystal colloids with an emphasis on experimental tools and applications of topology in condensed matter, as well as practical micro-photonics applications. It includes a number of spectacular manifestations of new topological phenomena not found or difficult to observe in other systems. Starting from the early works on nematic colloids, it explains the basics of topological defects in ordered media, charge and winding, and the elastic forces between colloidal particles in nematics. Following a detailed description of experimental methods, such as optical tweezing and particle tracking, the book eases the reader into the theoretical part, which de...

  1. Dosimetry for Crystals Irradiation

    CERN Document Server

    Lecomte, Pierre

    2005-01-01

    Before shipment to CMS, all PbWO4 crystals produced in China are irradiated there with 60 Co , in order to insure that the induced absorption coefficient is within specifications. Acceptance tests at CERNand at ENEA also include irradiation with gamma rays from 60 Co sources. There were initially discrepancies in quoted doses and doserates as well as in induced absorption coefficients. The present work resolves the discrepancies in irradiation measurements and defines common dosimetry methods for consistency checks between irradiation facilities.

  2. Crystals against cancer

    CERN Multimedia

    2009-01-01

    This is a remarkable example of direct technology transfer from particle physics to medicine. Clinical trials have begun in Portugal on a new medical imaging system for the diagnosis of breast cancer, which uses positron emission tomography (PET). The system, developed by a Portuguese consortium in collaboration with CERN and laboratories participating in the Crystal Clear collaboration, will detect even the smallest tumours and thus help avoid unnecessary biopsies.

  3. On crystallization of law

    Directory of Open Access Journals (Sweden)

    Szmodis Jenő

    2014-01-01

    Full Text Available The article introduces the problem of autonomy of law. The paper examines the medieval origins of legal positivism from a historical approach, sketching the main theories concerning the emergence of law, and phrasing some preliminary consideration for a historical and philosophical view of the problem of the birth of law. As a result of reasoning the article suggests some legal historical and human ethological ideas relating to the phenomena of crystallization of the law.

  4. Phononic crystals fundamentals and applications

    CERN Document Server

    Adibi, Ali

    2016-01-01

    This book provides an in-depth analysis as well as an overview of phononic crystals. This book discusses numerous techniques for the analysis of phononic crystals and covers, among other material, sonic and ultrasonic structures, hypersonic planar structures and their characterization, and novel applications of phononic crystals. This is an ideal book for those working with micro and nanotechnology, MEMS (microelectromechanical systems), and acoustic devices. This book also: Presents an introduction to the fundamentals and properties of phononic crystals Covers simulation techniques for the analysis of phononic crystals Discusses sonic and ultrasonic, hypersonic and planar, and three-dimensional phononic crystal structures Illustrates how phononic crystal structures are being deployed in communication systems and sensing systems.

  5. Quartz crystal fabrication facility

    Science.gov (United States)

    Ney, R. J.

    1980-05-01

    The report describes the design and operation of a five chamber, interconnected vacuum system, which is capable of cleaning, plating, and sealing precision quartz crystal units in ceramic flatpack enclosures continuously in a high vacuum environment. The production rate design goal was 200 units per eight hour day. A unique nozzle beam gold deposition source was developed to operate for extended periods of time without reloading. The source puts out a narrow beam of gold typically in the order of 2 1/2 deg included cone angle. Maximum deposition rates are in the order of 400 a/min at 5.5 in. 'throw' distance used. Entrance and exit air lock chambers expedite the material throughput, so that the processing chambers are at high vacuum for extended periods of time. A stainless steel conveyor belt, in conjunction with three vacuum manipulators, transport the resonator components to the various work stations. Individual chambers are normally separated from each other by gate valves. The crystal resonators, mounted in flatpack frames but unplated, are loaded into transport trays in a lid-frame-lid sequency for insertion into the system and exit as completed crystal units. The system utilizes molybdenum coated ball bearings at essentially all friction surfaces. The gold sources and plating mask heads are equipped with elevators and gate valves, so that they can be removed from the system for maintenance without exposing the chambers to atmosphere.

  6. Slotted Photonic Crystal Sensors

    Science.gov (United States)

    Scullion, Mark G.; Krauss, Thomas F.; Di Falco, Andrea

    2013-01-01

    Optical biosensors are increasingly being considered for lab-on-a-chip applications due to their benefits such as small size, biocompatibility, passive behaviour and lack of the need for fluorescent labels. The light guiding mechanisms used by many of them results in poor overlap of the optical field with the target molecules, reducing the maximum sensitivity achievable. This review article presents a new platform for optical biosensors, namely slotted photonic crystals, which provide higher sensitivities due to their ability to confine, spatially and temporally, the optical mode peak within the analyte itself. Loss measurements showed values comparable to standard photonic crystals, confirming their ability to be used in real devices. A novel resonant coupler was designed, simulated, and experimentally tested, and was found to perform better than other solutions within the literature. Combining with cavities, microfluidics and biological functionalization allowed proof-of-principle demonstrations of protein binding to be carried out. Higher sensitivities were observed in smaller structures than possible with most competing devices reported in the literature. This body of work presents slotted photonic crystals as a realistic platform for complete on-chip biosensing; addressing key design, performance and application issues, whilst also opening up exciting new ideas for future study. PMID:23503295

  7. Slotted Photonic Crystal Sensors

    Directory of Open Access Journals (Sweden)

    Andrea Di Falco

    2013-03-01

    Full Text Available Optical biosensors are increasingly being considered for lab-on-a-chip applications due to their benefits such as small size, biocompatibility, passive behaviour and lack of the need for fluorescent labels. The light guiding mechanisms used by many of them results in poor overlap of the optical field with the target molecules, reducing the maximum sensitivity achievable. This review article presents a new platform for optical biosensors, namely slotted photonic crystals, which provide higher sensitivities due to their ability to confine, spatially and temporally, the optical mode peak within the analyte itself. Loss measurements showed values comparable to standard photonic crystals, confirming their ability to be used in real devices. A novel resonant coupler was designed, simulated, and experimentally tested, and was found to perform better than other solutions within the literature. Combining with cavities, microfluidics and biological functionalization allowed proof-of-principle demonstrations of protein binding to be carried out. Higher sensitivities were observed in smaller structures than possible with most competing devices reported in the literature. This body of work presents slotted photonic crystals as a realistic platform for complete on-chip biosensing; addressing key design, performance and application issues, whilst also opening up exciting new ideas for future study.

  8. Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction

    International Nuclear Information System (INIS)

    Emamzadah, Soheila; Petty, Tom J.; De Almeida, Victor; Nishimura, Taisuke; Joly, Jacques; Ferrer, Jean-Luc; Halazonetis, Thanos D.

    2009-01-01

    A cyclic olefin homopolymer-based microfluidics system has been established for protein crystallization and in situ X-ray diffraction. Microfluidics is a promising technology for the rapid identification of protein crystallization conditions. However, most of the existing systems utilize silicone elastomers as the chip material which, despite its many benefits, is highly permeable to water vapour. This limits the time available for protein crystallization to less than a week. Here, the use of a cyclic olefin homopolymer-based microfluidics system for protein crystallization and in situ X-ray diffraction is described. Liquid handling in this system is performed in 2 mm thin transparent cards which contain 500 chambers, each with a volume of 320 nl. Microbatch, vapour-diffusion and free-interface diffusion protocols for protein crystallization were implemented and crystals were obtained of a number of proteins, including chicken lysozyme, bovine trypsin, a human p53 protein containing both the DNA-binding and oligomerization domains bound to DNA and a functionally important domain of Arabidopsis Morpheus’ molecule 1 (MOM1). The latter two polypeptides have not been crystallized previously. For X-ray diffraction analysis, either the cards were opened to allow mounting of the crystals on loops or the crystals were exposed to X-rays in situ. For lysozyme, an entire X-ray diffraction data set at 1.5 Å resolution was collected without removing the crystal from the card. Thus, cyclic olefin homopolymer-based microfluidics systems have the potential to further automate protein crystallization and structural genomics efforts

  9. Beyond DNA repair: DNA-PK function in cancer

    OpenAIRE

    Goodwin, Jonathan F.; Knudsen, Karen E.

    2014-01-01

    The DNA-dependent protein kinase (DNA-PK) is a pivotal component of the DNA repair machinery that governs the response to DNA damage, serving to maintain genome integrity. However, the DNA-PK kinase component was initially isolated with transcriptional complexes, and recent findings have illuminated the impact of DNA-PK-mediated transcriptional regulation on tumor progression and therapeutic response. DNA-PK expression has also been correlated with poor outcome in selected tumor types, furthe...

  10. On dewetting of thin films due to crystallization (crystallization dewetting).

    Science.gov (United States)

    Habibi, Mehran; Rahimzadeh, Amin; Eslamian, Morteza

    2016-03-01

    Drying and crystallization of a thin liquid film of an ionic or a similar solution can cause dewetting in the resulting thin solid film. This paper aims at investigating this type of dewetting, herein termed "crystallization dewetting", using PbI2 dissolved in organic solvents as the model solution. PbI2 solid films are usually used in X-ray detection and lead halide perovskite solar cells. In this work, PbI2 films are fabricated using spin coating and the effect of major parameters influencing the crystallization dewetting, including the type of the solvent, solution concentration, drying temperature, spin speed, as well as imposed vibration on the substrate are studied on dewetting, surface profile and coverage, using confocal scanning laser microscopy. Simplified hydrodynamic governing equations of crystallization in thin films are presented and using a mathematical representation of the process, it is phenomenologically demonstrated that crystallization dewetting occurs due to the absorption and consumption of the solution surrounding a growing crystal. Among the results, it is found that a low spin speed (high thickness), a high solution concentration and a low drying temperature promote crystal growth, and therefore crystallization dewetting. It is also shown that imposed vibration on the substrate can affect the crystal size and crystallization dewetting.

  11. DNA topology and transcription

    Science.gov (United States)

    Kouzine, Fedor; Levens, David; Baranello, Laura

    2014-01-01

    Chromatin is a complex assembly that compacts DNA inside the nucleus while providing the necessary level of accessibility to regulatory factors conscripted by cellular signaling systems. In this superstructure, DNA is the subject of mechanical forces applied by variety of molecular motors. Rather than being a rigid stick, DNA possesses dynamic structural variability that could be harnessed during critical steps of genome functioning. The strong relationship between DNA structure and key genomic processes necessitates the study of physical constrains acting on the double helix. Here we provide insight into the source, dynamics, and biology of DNA topological domains in the eukaryotic cells and summarize their possible involvement in gene transcription. We emphasize recent studies that might inspire and impact future experiments on the involvement of DNA topology in cellular functions. PMID:24755522

  12. Eukaryotic DNA Replication Fork.

    Science.gov (United States)

    Burgers, Peter M J; Kunkel, Thomas A

    2017-06-20

    This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

  13. Unifying the crystallization behavior of hexagonal and square crystals with the phase-field-crystal model

    International Nuclear Information System (INIS)

    Yang Tao; Chen Zheng; Zhang Jing; Wang Yongxin; Lu Yanli

    2016-01-01

    By employing the phase-field-crystal models, the atomic crystallization process of hexagonal and square crystals is investigated with the emphasis on the growth mechanism and morphological change. A unified regime describing the crystallization behavior of both crystals is obtained with the thermodynamic driving force varying. By increasing the driving force, both crystals (in the steady-state) transform from a faceted polygon to an apex-bulged polygon, and then into a symmetric dendrite. For the faceted polygon, the interface advances by a layer-by-layer (LL) mode while for the apex-bulged polygonal and the dendritic crystals, it first adopts the LL mode and then transits into the multi-layer (ML) mode in the later stage. In particular, a shift of the nucleation sites from the face center to the area around the crystal tips is detected in the early growth stage of both crystals and is rationalized in terms of the relation between the crystal size and the driving force distribution. Finally, a parameter characterizing the complex shape change of square crystal is introduced. (paper)

  14. DNA-based machines.

    Science.gov (United States)

    Wang, Fuan; Willner, Bilha; Willner, Itamar

    2014-01-01

    The base sequence in nucleic acids encodes substantial structural and functional information into the biopolymer. This encoded information provides the basis for the tailoring and assembly of DNA machines. A DNA machine is defined as a molecular device that exhibits the following fundamental features. (1) It performs a fuel-driven mechanical process that mimics macroscopic machines. (2) The mechanical process requires an energy input, "fuel." (3) The mechanical operation is accompanied by an energy consumption process that leads to "waste products." (4) The cyclic operation of the DNA devices, involves the use of "fuel" and "anti-fuel" ingredients. A variety of DNA-based machines are described, including the construction of "tweezers," "walkers," "robots," "cranes," "transporters," "springs," "gears," and interlocked cyclic DNA structures acting as reconfigurable catenanes, rotaxanes, and rotors. Different "fuels", such as nucleic acid strands, pH (H⁺/OH⁻), metal ions, and light, are used to trigger the mechanical functions of the DNA devices. The operation of the devices in solution and on surfaces is described, and a variety of optical, electrical, and photoelectrochemical methods to follow the operations of the DNA machines are presented. We further address the possible applications of DNA machines and the future perspectives of molecular DNA devices. These include the application of DNA machines as functional structures for the construction of logic gates and computing, for the programmed organization of metallic nanoparticle structures and the control of plasmonic properties, and for controlling chemical transformations by DNA machines. We further discuss the future applications of DNA machines for intracellular sensing, controlling intracellular metabolic pathways, and the use of the functional nanostructures for drug delivery and medical applications.

  15. DNA repair and cancer

    International Nuclear Information System (INIS)

    Rathore, Shakuntla; Joshi, Pankaj Kumar; Gaur, Sudha

    2012-01-01

    DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecule that encode it's genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many one million individual molecular lesions per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions include potentially harmful mutation in cell's genome which affect the survival of it's daughter cells after it undergoes mitosis. As a consequence, the DNA repair process is constantly active as it responds to damage in the DNA structure. Inherited mutation that affect DNA repair genes are strongly associated with high cancer risks in humans. Hereditary non polyposis colorectal cancer (HNPCC) is strongly associated with specific mutation in the DNA mismatch repair pathway. BRCA1, BRCA2 two famous mutation conferring a hugely increased risk of breast cancer on carrier, are both associated with a large number of DNA repair pathway, especially NHEJ and homologous recombination. Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the capacity of the cell to repair DNA damage, resulting in cell death. Cells that are most rapidly dividing most typically cancer cells are preferentially affected. The side effect is that other non-cancerous but rapidly dividing cells such as stem cells in the bone marrow are also affected. Modern cancer treatment attempt to localize the DNA damage to cells and tissue only associated with cancer, either by physical means (concentrating the therapeutic agent in the region of the tumor) or by biochemical means (exploiting a feature unique to cancer cells in the body). (author)

  16. Nonisotopic DNA probe techniques

    National Research Council Canada - National Science Library

    Kricka, Larry J

    1992-01-01

    The objective of this book is to bring together descriptions of the principal nonisotopic methods for DNA hybridization assays, together with experimental details of the methods, including labelling...

  17. DNA replication and cancer

    DEFF Research Database (Denmark)

    Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

    2016-01-01

    A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

  18. Forensic DNA testing.

    Science.gov (United States)

    Butler, John M

    2011-12-01

    Forensic DNA testing has a number of applications, including parentage testing, identifying human remains from natural or man-made disasters or terrorist attacks, and solving crimes. This article provides background information followed by an overview of the process of forensic DNA testing, including sample collection, DNA extraction, PCR amplification, short tandem repeat (STR) allele separation and sizing, typing and profile interpretation, statistical analysis, and quality assurance. The article concludes with discussions of possible problems with the data and other forensic DNA testing techniques.

  19. Fluid Physics and Macromolecular Crystal Growth in Microgravity

    Science.gov (United States)

    Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    " is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

  20. Structure of DNA toroids and electrostatic attraction of DNA duplexes

    International Nuclear Information System (INIS)

    Cherstvy, A G

    2005-01-01

    DNA-DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge distribution and favours hexagonal toroidal cross-sections. The latter is in agreement with recent cryo-electron microscopy studies on DNA condensed with cobalt hexammine. We treat the DNA-DNA interactions within the modern theory of electrostatic interaction between helical macromolecules. The size and thickness of the toroids is calculated within a simple model; other models of stability of DNA toroids are discussed and compared

  1. Principles of crystallization, and methods of single crystal growth

    International Nuclear Information System (INIS)

    Chacra, T.

    2010-01-01

    Most of single crystals (monocrystals), have distinguished optical, electrical, or magnetic properties, which make from single crystals, key elements in most of technical modern devices, as they may be used as lenses, Prisms, or grating sin optical devises, or Filters in X-Ray and spectrographic devices, or conductors and semiconductors in electronic, and computer industries. Furthermore, Single crystals are used in transducer devices. Moreover, they are indispensable elements in Laser and Maser emission technology.Crystal Growth Technology (CGT), has started, and developed in the international Universities and scientific institutions, aiming at some of single crystals, which may have significant properties and industrial applications, that can attract the attention of international crystal growth centers, to adopt the industrial production and marketing of such crystals. Unfortunately, Arab universities generally, and Syrian universities specifically, do not give even the minimum interest, to this field of Science.The purpose of this work is to attract the attention of Crystallographers, Physicists and Chemists in the Arab universities and research centers to the importance of crystal growth, and to work on, in the first stage to establish simple, uncomplicated laboratories for the growth of single crystal. Such laboratories can be supplied with equipment, which are partly available or can be manufactured in the local market. Many references (Articles, Papers, Diagrams, etc..) has been studied, to conclude the most important theoretical principles of Phase transitions,especially of crystallization. The conclusions of this study, are summarized in three Principles; Thermodynamic-, Morphologic-, and Kinetic-Principles. The study is completed by a brief description of the main single crystal growth methods with sketches, of equipment used in each method, which can be considered as primary designs for the equipment, of a new crystal growth laboratory. (author)

  2. Logical NAND and NOR Operations Using Algorithmic Self-assembly of DNA Molecules

    Science.gov (United States)

    Wang, Yanfeng; Cui, Guangzhao; Zhang, Xuncai; Zheng, Yan

    DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated for programmable construction of patterned systems on the molecular scale. It has been demonstrated that the simple binary arithmetic and logical operations can be computed by the process of self assembly of DNA tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules that can be used to execute five steps of a logical NAND and NOR operations on a string of binary bits. To achieve this, abstract tiles were translated into DNA tiles based on triple-crossover motifs. Serving as input for the computation, long single stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. Our method shows that engineered DNA self-assembly can be treated as a bottom-up design techniques, and can be capable of designing DNA computer organization and architecture.

  3. Crystal structure and magnetic susceptibility of UOSe single crystals

    International Nuclear Information System (INIS)

    Kaczorowski, D.; Muenster Univ.; Poettgen, R.; Jeitschko, W.; Gajek, Z.; Zygmunt, A.

    1993-01-01

    The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T N =100±2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author)

  4. Crystal structure and magnetic susceptibility of UOSe single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Kaczorowski, D. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Poettgen, R.; Jeitschko, W. (Muenster Univ. (Germany). Anorganisch-Chemisches Inst.); Gajek, Z.; Zygmunt, A. (Polish Academy of Sciences, Wroclaw (Poland). Inst. for Low Temperature and Structure Research)

    1993-01-01

    The crystal structure and magnetic susceptibility behaviour of UOSe single crystals have been studied. UOSe crystalizes in the tetragonal PbFC1-type structure (space group P4/nmm) with the lattice parameters: a = 390.38(5) pm and c = 698.05(9) pm. It orders antiferromagnetically at T[sub N]=100[+-]2 K and exhibits a very strong anisotropy in the susceptibility vs temperature variation. The magnetic and thermodynamic properties of UOSe are successfully interpreted in the framework of a perturbative ab initio crystal field approach. (Author).

  5. Charge-transfer interactions of Cr species with DNA.

    Science.gov (United States)

    Nowicka, Anna M; Matysiak-Brynda, Edyta; Hepel, Maria

    2017-10-01

    Interactions of Cr species with nucleic acids in living organisms depend strongly on Cr oxidation state and the environmental conditions. As the effects of these interactions range from benign to pre-mutagenic to carcinogenic, careful assessment of the hazard they pose to human health is necessary. We have investigated methods that would enable quantifying the DNA damage caused by Cr species under varying environmental conditions, including UV, O 2 , and redox potential, using simple instrumental techniques which could be in future combined into a field-deployable instrumentation. We have employed electrochemical quartz crystal nanogravimetry (EQCN), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) to evaluate the extent of DNA damage expressed in terms of guanine oxidation yield (η) and changes in specific characteristics provided by these techniques. The effects of the interactions of Cr species with DNA were analyzed using a model calf thymus DNA (ctDNA) film on a gold electrode (Au@ctDNA) in different media, including: (i) Cr(VI), (ii) Cr(VI) reduced at -0.2V, (iii) Cr(III)+UV radiation+O 2 , and Cr(III), obtaining the η values: 7.4±1.4, 1.5±0.4, 1.1±0.31%, and 0%, respectively, thus quantifying the hazard posed. The EIS measurements have enabled utilizing the decrease in charge-transfer resistance (R ct ) for ferri/ferrocyanide redox probe at an Au@ctDNA electrode to assess the oxidative ctDNA damage by Cr(VI) species. In this case, circular dichroism indicates an extensive damage to the ctDNA hydrogen bonding. On the other hand, Cr(III) species have not induced any damage to ctDNA, although the EQCN measurements show an electrostatic binding to DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

  6. Crystallized Schroedinger cat states

    International Nuclear Information System (INIS)

    Castanos, O.; Lopez-Pena, R.; Man'ko, V.I.

    1995-01-01

    Crystallized Schroedinger cat states (male and female) are introduced on the base of extension of group construction for the even and odd coherent states of the electromagnetic field oscillator. The Wigner and Q functions are calculated and some are plotted for C 2 , C 3 , C 4 , C 5 , C 3v Schroedinger cat states. Quadrature means and dispersions for these states are calculated and squeezing and correlation phenomena are studied. Photon distribution functions for these states are given explicitly and are plotted for several examples. A strong oscillatory behavior of the photon distribution function for some field amplitudes is found in the new type of states

  7. Crystal structure of cafenstrole

    Directory of Open Access Journals (Sweden)

    Gihaeng Kang

    2015-08-01

    Full Text Available The title compound (systematic name: N,N-diethyl-3-mesitylsulfonyl-1H-1,2,4-triazole-1-carboxamide, C16H22N4O3S, is a triazole herbicide. The dihedral angle between the planes of the triazole and benzene ring planes is 88.14 (10°. In the crystal, C—H...O hydrogen bonds and weak C—H...π interactions link adjacent molecules, forming one-dimensional chains along the a axis.

  8. Liquid Crystal Airborne Display

    Science.gov (United States)

    1977-08-01

    Cum.nings, J. P., et al., Properties and Limitations oe Liquid Crystals for Aircraft Displays, Honeywell Corporate Researc ."I Center, Final Report HR-72...basic module could be used to build displays for both the commercial and military! 157- marhecs, and so would establi sh a broad and sizable market ... market for the display becomes a reality; therein lies, f TABLE 16 THE COURSE OF FUTURE DISPLAY DEVELOPMENT Today 1976-77 1980 1985 Display Size 2" 1 3.2

  9. Crystal structure of pseudoguainolide

    Directory of Open Access Journals (Sweden)

    Noureddine Beghidja

    2015-03-01

    Full Text Available The lactone ring in the title molecule, C15H22O3 (systematic name: 3,4a,8-trimethyldodecahydroazuleno[6,5-b]furan-2,5-dione, assumes an envelope conformation with the methine C atom adjacent to the the methine C atom carrying the methyl substituent being the flap atom. The other five-membered ring adopts a twisted conformation with the twist being about the methine–methylene C—C bond. The seven-membered ring is based on a twisted boat conformation. No specific interactions are noted in the the crystal packing.

  10. Radiation Damage in Scintillating Crystals

    CERN Document Server

    Zhu Ren Yuan

    1998-01-01

    Crystal Calorimetry in future high energy physics experiments faces a new challenge to maintain its precision in a hostile radiation environment. This paper discusses the effects of radiation damage in scintillating crystals, and concludes that the predominant radiation damage effect in crystal scintillators is the radiation induced absorption, or color center formation, not the loss of the scintillation light yield. The importance of maintaining crystal's light response uniformity and the feasibility to build a precision crystal calorimeter under radiation are elaborated. The mechanism of the radiation damage in scintillating crystals is also discussed. While the damage in alkali halides is found to be caused by the oxygen or hydroxyl contamination, it is the structure defects, such as oxygen vacancies, cause damage in oxides. Material analysis methods used to reach these conclusions are presented in details.

  11. Hopper Growth of Salt Crystals.

    Science.gov (United States)

    Desarnaud, Julie; Derluyn, Hannelore; Carmeliet, Jan; Bonn, Daniel; Shahidzadeh, Noushine

    2018-06-07

    The growth of hopper crystals is observed for many substances, but the mechanism of their formation remains ill understood. Here we investigate their growth by performing evaporation experiments on small volumes of salt solutions. We show that sodium chloride crystals that grow very fast from a highly supersaturated solution form a peculiar form of hopper crystal consisting of a series of connected miniature versions of the original cubic crystal. The transition between cubic and such hopper growth happens at a well-defined supersaturation where the growth rate of the cubic crystal reaches a maximum (∼6.5 ± 1.8 μm/s). Above this threshold, the growth rate varies as the third power of supersaturation, showing that a new mechanism, controlled by the maximum speed of surface integration of new molecules, induces the hopper growth of cubic crystals in cascade.

  12. Quasimetallic silicon micromachined photonic crystals

    International Nuclear Information System (INIS)

    Temelkuran, B.; Bayindir, Mehmet; Ozbay, E.; Kavanaugh, J. P.; Sigalas, M. M.; Tuttle, G.

    2001-01-01

    We report on fabrication of a layer-by-layer photonic crystal using highly doped silicon wafers processed by semiconductor micromachining techniques. The crystals, built using (100) silicon wafers, resulted in an upper stop band edge at 100 GHz. The transmission and defect characteristics of these structures were found to be analogous to metallic photonic crystals. We also investigated the effect of doping concentration on the defect characteristics. The experimental results agree well with predictions of the transfer matrix method simulations

  13. Extended DNA Tile Actuators

    DEFF Research Database (Denmark)

    Kristiansen, Martin; Kryger, Mille; Zhang, Zhao

    2012-01-01

    A dynamic linear DNA tile actuator is expanded to three new structures of higher complexity. The original DNA actuator was constructed from a central roller strand which hybridizes with two piston strands by forming two half-crossover junctions. A linear expansion of the actuator is obtained...

  14. Dna fingerprinting - review paper

    OpenAIRE

    Blundell, Renald

    2006-01-01

    Before the Polymerase Chain Reaction (PCR) was established, DNA fingerprinting technology has relied for years on Restriction Fragment Length Polymorphism (RFLP) and Variable Number of Tandom Repeats (VNTR) analysis, a very efficient technique but quite laborious and not suitable for high throughput mapping. Since its, development, PCR has provided a new and powerful tool for DNA fingerprinting.

  15. DNA Repair Systems

    Indian Academy of Sciences (India)

    Thanks to the pioneering research work of Lindahl, Sancar, Modrich and their colleagues, we now have an holistic awareness of how DNA damage occurs and how the damage is rectified in bacteria as well as in higher organisms including human beings. A comprehensive understanding of DNA repair has proven crucial ...

  16. DNA repair genes

    International Nuclear Information System (INIS)

    Morimyo, Mitsuoki

    1995-01-01

    Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

  17. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2018-05-15

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  18. Characterization of muntjac DNA

    International Nuclear Information System (INIS)

    Davis, R.C.

    1981-01-01

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange

  19. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  20. Characterization of muntjac DNA

    Energy Technology Data Exchange (ETDEWEB)

    Davis, R.C.

    1981-05-27

    Sister chromatid exchange (SCE) in muntjac chromosomes is generally proportional to the chromosomal DNA content, but the SCE frequency is reduced in the heterochromatic neck region of the X chromosome. The physical properties of muntjac DNA and the kinetics of repair of UV damage in muntjac heterochromatin and euchromatin were examined and compared with the distribution of sister chromatid exchange.

  1. Aluminum-air battery crystallizer

    Science.gov (United States)

    Maimoni, A.

    1987-01-01

    A prototype crystallizer system for the aluminum-air battery operated reliably through simulated startup and shutdown cycles and met its design objectives. The crystallizer system allows for crystallization and removal of the aluminium hydroxide reaction product; it is required to allow steady-state and long-term operation of the aluminum-air battery. The system has to minimize volume and maintain low turbulence and shear to minimize secondary nucleation and energy consumption while enhancing agglomeration. A lamella crystallizer satisfies system constraints.

  2. Physical Properties of Liquid Crystals

    CERN Document Server

    Gray, George W; Spiess, Hans W

    1999-01-01

    This handbook is a unique compendium of knowledge on all aspects of the physics of liquid crystals. In over 500 pages it provides detailed information on the physical properties of liquid crystals as well as the recent theories and results on phase transitions, defects and textures of different types of liquid crystals. An in-depth understanding of the physical fundamentals is a prerequisite for everyone working in the field of liquid crystal research. With this book the experts as well as graduate students entering the field get all the information they need.

  3. Wetting of cholesteric liquid crystals.

    Science.gov (United States)

    Silvestre, Nuno M; Figueirinhas Pereira, Maria Carolina; Bernardino, Nelson R; Telo da Gama, Margarida M

    2016-02-01

    We investigate theoretically the wetting properties of cholesteric liquid crystals at a planar substrate. If the properties of substrate and of the interface are such that the cholesteric layers are not distorted, the wetting properties are similar to those of a nematic liquid crystal. If, on the other hand, the anchoring conditions force the distortion of the liquid crystal layers the wetting properties are altered, the free cholesteric-isotropic interface is non-planar and there is a layer of topological defects close to the substrate. These deformations can either promote or hinder the wetting of the substrate by a cholesteric, depending on the properties of the cholesteric liquid crystal.

  4. Preventing Crystal Agglomeration of Pharmaceutical Crystals Using Temperature Cycling and a Novel Membrane Crystallization Procedure for Seed Crystal Generation

    Directory of Open Access Journals (Sweden)

    Elena Simone

    2018-01-01

    Full Text Available In this work, a novel membrane crystallization system was used to crystallize micro-sized seeds of piroxicam monohydrate by reverse antisolvent addition. Membrane crystallization seeds were compared with seeds produced by conventional antisolvent addition and polymorphic transformation of a fine powdered sample of piroxicam form I in water. The membrane crystallization process allowed for a consistent production of pure monohydrate crystals with narrow size distribution and without significant agglomeration. The seeds were grown in 350 g of 20:80 w/w acetone-water mixture. Different seeding loads were tested and temperature cycling was applied in order to avoid agglomeration of the growing crystals during the process. Focused beam reflectance measurement (FBRM; and particle vision and measurement (PVM were used to monitor crystal growth; nucleation and agglomeration during the seeded experiments. Furthermore; Raman spectroscopy was used to monitor solute concentration and estimate the overall yield of the process. Membrane crystallization was proved to be the most convenient and consistent method to produce seeds of highly agglomerating compounds; which can be grown via cooling crystallization and temperature cycling.

  5. Inelastic light scattering in crystals

    Science.gov (United States)

    Sushchinskii, M. M.

    The papers presented in this volume are concerned with a variety of problems in optics and solid state physics, such as Raman scattering of light in crystals and disperse media, Rayleigh and inelastic scattering during phase transitions, characteristics of ferroelectrics in relation to the general soft mode concept, and inelastic spectral opalescence. A group-theory approach is used to classify the vibrational spectra of the crystal lattice and to analyze the properties of idealized crystal models. Particular attention is given to surface vibrational states and to the study of the surface layers of crystals and films by light scattering methods.

  6. Whose DNA is this?

    DEFF Research Database (Denmark)

    Taroni, Franco; Biedermann, Alex; Vuille, Joëlle

    2013-01-01

    This communication seeks to draw the attention of researchers and practitioners dealing with forensic DNA profiling analyses to the following question: is a scientist's report, offering support to a hypothesis according to which a particular individual is the source of DNA detected during...... evoked during the international conference "The hidden side of DNA profiles. Artifacts, errors and uncertain evidence" held in Rome (April 27th to 28th, 2012). Indeed, despite the fact that this conference brought together some of the world's leading forensic DNA specialists, it appeared clearly...... talk considerably different languages. It thus is fundamental to address this issue of communication about results of forensic DNA analyses, and open a dialogue with practicing non-scientists at large who need to make meaningful use of scientific results to approach and help solve judicial cases...

  7. DNA repair protocols

    DEFF Research Database (Denmark)

    Bjergbæk, Lotte

    In its 3rd edition, this Methods in Molecular Biology(TM) book covers the eukaryotic response to genomic insult including advanced protocols and standard techniques in the field of DNA repair. Offers expert guidance for DNA repair, recombination, and replication. Current knowledge of the mechanisms...... that regulate DNA repair has grown significantly over the past years with technology advances such as RNA interference, advanced proteomics and microscopy as well as high throughput screens. The third edition of DNA Repair Protocols covers various aspects of the eukaryotic response to genomic insult including...... recent advanced protocols as well as standard techniques used in the field of DNA repair. Both mammalian and non-mammalian model organisms are covered in the book, and many of the techniques can be applied with only minor modifications to other systems than the one described. Written in the highly...

  8. Tunable Topological Phononic Crystals

    KAUST Repository

    Chen, Zeguo; Wu, Ying

    2016-01-01

    Topological insulators first observed in electronic systems have inspired many analogues in photonic and phononic crystals in which remarkable one-way propagation edge states are supported by topologically nontrivial band gaps. Such band gaps can be achieved by breaking the time-reversal symmetry to lift the degeneracy associated with Dirac cones at the corners of the Brillouin zone. Here, we report on our construction of a phononic crystal exhibiting a Dirac-like cone in the Brillouin zone center. We demonstrate that simultaneously breaking the time-reversal symmetry and altering the geometric size of the unit cell result in a topological transition that we verify by the Chern number calculation and edge-mode analysis. We develop a complete model based on the tight binding to uncover the physical mechanisms of the topological transition. Both the model and numerical simulations show that the topology of the band gap is tunable by varying both the velocity field and the geometric size; such tunability may dramatically enrich the design and use of acoustic topological insulators.

  9. Crystal growth and doping

    International Nuclear Information System (INIS)

    Paorici, C.

    1980-01-01

    Section 1 contains a self-consistent review of the basic growth features. After a short introduction concerning the driving force acting in a crystallization process, three main topics are broadly discussed: (i) interface kinetics; (ii) transport kinetics, and (iii) growth stability conditions. On point (i), after definition of the nature of interface, using Temkin's model, the growth mechanisms predicted by Burton, Cabrera and Frank (BCF) and bidimensional nucleation theories are fully developed. On points (ii) and (iii), the differential equations of the constitutional (concentration) and thermal fields are presented and discussed in terms of relevant approximations, suitable boundary conditions and limit values expected in order to have growth stability. Section 2 reports various experimental procedures for growing bulk crystals from the melt, from solutions and from the vapour phase. The basic concepts of Section 1 are amply employed for a critical discussion of possibilities, advantages and drawbacks of the methods described. Along the same lines, in Section 3 the principal epitaxial deposition procedures are highlighted. Section 4 contains a brief account of doping and of stoichiometry-defect control procedures. There is a long, carefully chosen list of bibliographical references. (author)

  10. Liquid Crystals in Tribology

    Directory of Open Access Journals (Sweden)

    María-Dolores Bermúdez

    2009-09-01

    Full Text Available Two decades ago, the literature dealing with the possible applications of low molar mass liquid crystals, also called monomer liquid crystals (MLCs, only included about 50 references. Today, thousands of papers, conference reports, books or book chapters and patents refer to the study and applications of MLCs as lubricants and lubricant additives and efforts are made to develop new commercial applications. The development of more efficient lubricants is of paramount technological and economic relevance as it is estimated that half the energy consumption is dissipated as friction. MLCs have shown their ability to form ordered boundary layers with good load-carrying capacity and to lower the friction coefficients, wear rates and contact temperature of sliding surfaces, thus contributing to increase the components service life and to save energy. This review includes the use of MLCs in lubrication, and dispersions of MLCs in conventional polymers (PDMLCs. Finally, new lubricating system composed of MLC blends with surfactants, ionic liquids or nanophases are considered.

  11. Tunable Topological Phononic Crystals

    KAUST Repository

    Chen, Zeguo

    2016-05-27

    Topological insulators first observed in electronic systems have inspired many analogues in photonic and phononic crystals in which remarkable one-way propagation edge states are supported by topologically nontrivial band gaps. Such band gaps can be achieved by breaking the time-reversal symmetry to lift the degeneracy associated with Dirac cones at the corners of the Brillouin zone. Here, we report on our construction of a phononic crystal exhibiting a Dirac-like cone in the Brillouin zone center. We demonstrate that simultaneously breaking the time-reversal symmetry and altering the geometric size of the unit cell result in a topological transition that we verify by the Chern number calculation and edge-mode analysis. We develop a complete model based on the tight binding to uncover the physical mechanisms of the topological transition. Both the model and numerical simulations show that the topology of the band gap is tunable by varying both the velocity field and the geometric size; such tunability may dramatically enrich the design and use of acoustic topological insulators.

  12. Crystal Compton Camera

    Energy Technology Data Exchange (ETDEWEB)

    Ziock, Klaus-Peter [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Braverman, Joshua B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Harrison, Mark J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hornback, Donald Eric [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fabris, Lorenzo [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Newby, Jason [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-09-26

    Stand-off detection is one of the most important radiation detection capabilities for arms control and the control of illicit nuclear materials. For long range passive detection one requires a large detector and a means of “seeing through” the naturally occurring and varying background radiation, i.e. imaging. Arguably, Compton imaging is the best approach over much of the emission band suitable for long range detection. It provides not only imaging, but more information about the direction of incidence of each detected gamma-ray than the alternate approach of coded-aperture imaging. The directional information allows one to reduce the background and hence improve the sensitivity of a measurement. However, to make an efficient Compton imager requires localizing and measuring the simultaneous energy depositions when gamma-rays Compton scatter and are subsequently captured within a single, large detector volume. This concept has been demonstrated in semi-conductor detectors (HPGe, CZT, Si) but at ~ $1k/cm3 these materials are too expensive to build the large systems needed for standoff detection. Scintillator detectors, such as NaI(Tl), are two orders of magnitude less expensive and possess the energy resolution required to make such an imager. However, they do not currently have the ability to localize closely spaced, simultaneous energy depositions in a single large crystal. In this project we are applying a new technique that should, for the first time ever, allow cubic-millimeter event localization in a bulk scintillator crystal.

  13. Electron spectroscopy of crystals

    CERN Document Server

    Nemoshkalenko, V V

    1979-01-01

    This book is conceived as a monograph, and represents an up-to-date collection of information concerning the use of the method of X-ray photoelectron spec­ troscopy in the study of the electron structure of crystals, as well as a personal interpretation of the subject by the authors. In a natural way, the book starts in Chapter 1 with a recapitulation of the fundamentals of the method, basic relations, principles of operation, and a com­ parative presentation of the characteristics and performances of the most com­ monly used ESCA instruments (from the classical ones-Varian, McPherson, Hewlett Packard, and IEEE-up to the latest model developed by Professor Siegbahn in Uppsala), and continues with a discussion of some of the difficult problems the experimentalist must face such as calibration of spectra, prepara­ tion of samples, and evaluation of the escape depth of electrons. The second chapter is devoted to the theory of photoemission from crystal­ line solids. A discussion of the methods of Hartree-Fo...

  14. Reconfigurable topological photonic crystal

    Science.gov (United States)

    Shalaev, Mikhail I.; Desnavi, Sameerah; Walasik, Wiktor; Litchinitser, Natalia M.

    2018-02-01

    Topological insulators are materials that conduct on the surface and insulate in their interior due to non-trivial topology of the band structure. The edge states on the interface between topological (non-trivial) and conventional (trivial) insulators are topologically protected from scattering due to structural defects and disorders. Recently, it was shown that photonic crystals (PCs) can serve as a platform for realizing a scatter-free propagation of light waves. In conventional PCs, imperfections, structural disorders, and surface roughness lead to significant losses. The breakthrough in overcoming these problems is likely to come from the synergy of the topological PCs and silicon-based photonics technology that enables high integration density, lossless propagation, and immunity to fabrication imperfections. For many applications, reconfigurability and capability to control the propagation of these non-trivial photonic edge states is essential. One way to facilitate such dynamic control is to use liquid crystals (LCs), which allow to modify the refractive index with external electric field. Here, we demonstrate dynamic control of topological edge states by modifying the refractive index of a LC background medium. Background index is changed depending on the orientation of a LC, while preserving the topology of the system. This results in a change of the spectral position of the photonic bandgap and the topological edge states. The proposed concept might be implemented using conventional semiconductor technology, and can be used for robust energy transport in integrated photonic devices, all-optical circuity, and optical communication systems.

  15. High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.

    Science.gov (United States)

    Baños-Mateos, Soledad; van Roon, Anne-Marie M; Lang, Ulla F; Maslen, Sarah L; Skehel, J Mark; Lamers, Meindert H

    2017-10-11

    High-fidelity DNA replication depends on a proofreading 3'-5' exonuclease that is associated with the replicative DNA polymerase. The replicative DNA polymerase DnaE1 from the major pathogen Mycobacterium tuberculosis (Mtb) uses its intrinsic PHP-exonuclease that is distinct from the canonical DEDD exonucleases found in the Escherichia coli and eukaryotic replisomes. The mechanism of the PHP-exonuclease is not known. Here, we present the crystal structure of the Mtb DnaE1 polymerase. The PHP-exonuclease has a trinuclear zinc center, coordinated by nine conserved residues. Cryo-EM analysis reveals the entry path of the primer strand in the PHP-exonuclease active site. Furthermore, the PHP-exonuclease shows a striking similarity to E. coli endonuclease IV, which provides clues regarding the mechanism of action. Altogether, this work provides important insights into the PHP-exonuclease and reveals unique properties that make it an attractive target for novel anti-mycobacterial drugs.The polymerase and histidinol phosphatase (PHP) domain in the DNA polymerase DnaE1 is essential for mycobacterial high-fidelity DNA replication. Here, the authors determine the DnaE1 crystal structure, which reveals the PHP-exonuclease mechanism that can be exploited for antibiotic development.

  16. Optics of globular photonic crystals

    International Nuclear Information System (INIS)

    Gorelik, V S

    2007-01-01

    The results of experimental and theoretical studies of the optical properties of globular photonic crystals - new physical objects having a crystal structure with the lattice period exceeding considerably the atomic size, are presented. As globular photonic crystals, artificial opal matrices consisting of close-packed silica globules of diameter ∼200 nm were used. The reflection spectra of these objects characterising the parameters of photonic bands existing in these crystals in the visible spectral region are presented. The idealised models of the energy band structure of photonic crystals investigated in the review give analytic dispersion dependences for the group velocity and the effective photon mass in a globular photonic crystal. The characteristics of secondary emission excited in globular photonic crystals by monochromatic and broadband radiation are presented. The results of investigations of single-photon-excited delayed scattering of light observed in globular photonic crystals exposed to cw UV radiation and radiation from a repetitively pulsed copper vapour laser are presented. The possibilities of using globular photonic crystals as active media for lasing in different spectral regions are considered. It is proposed to use globular photonic crystals as sensitive sensors in optoelectronic devices for molecular analysis of organic and inorganic materials by the modern methods of laser spectroscopy. The results of experimental studies of spontaneous and stimulated globular scattering of light are discussed. The conditions for observing resonance and two-photon-excited delayed scattering of light are found. The possibility of accumulation and localisation of the laser radiation energy inside a globular photonic crystal is reported. (review)

  17. Sequence-dependent DNA deformability studied using molecular dynamics simulations.

    Science.gov (United States)

    Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

    2007-01-01

    Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

  18. Nanostructures via DNA scaffold metallization

    OpenAIRE

    Ning, C.; Zinchenko, A.; Baigl, D.; Pyshkina, O.; Sergeyev, V.; Endo, Kazunaka; Yoshikawa, K.

    2005-01-01

    The critical role of polymers in process of noble metals nanostructures formation is well known, however, the use of DNA chain template in this process is yet largely unknown. In this study we demonstrate different ways of silver deposition on DNA template and report the influence of silver nanostructures formation on DNA conformational state. Metallization of DNA chain proceeds by two different scenarios depending on DNA conformation. If DNA chain is unfolded (elongated) chain, silver reduct...

  19. The Morse code effect: A crystal-crystal transformation observed in gel-grown lead (II) oxalate crystals

    Science.gov (United States)

    Lisgarten, J. N.; Marks, J. A.

    2018-05-01

    This paper reports on an unusual crystal-crystal transformation phenomenon, which we have called the Morse Code Effect, based on the change in appearance of lead(II) oxalate crystals grown in agarose gels.

  20. DNA damage and polyploidization.

    Science.gov (United States)

    Chow, Jeremy; Poon, Randy Y C

    2010-01-01

    A growing body of evidence indicates that polyploidization triggers chromosomal instability and contributes to tumorigenesis. DNA damage is increasingly being recognized for its roles in promoting polyploidization. Although elegant mechanisms known as the DNA damage checkpoints are responsible for halting the cell cycle after DNA damage, agents that uncouple the checkpoints can induce unscheduled entry into mitosis. Likewise, defects of the checkpoints in several disorders permit mitotic entry even in the presence of DNA damage. Forcing cells with damaged DNA into mitosis causes severe chromosome segregation defects, including lagging chromosomes, chromosomal fragments and chromosomal bridges. The presence of these lesions in the cleavage plane is believed to abort cytokinesis. It is postulated that if cytokinesis failure is coupled with defects of the p53-dependent postmitotic checkpoint pathway, cells can enter S phase and become polyploids. Progress in the past several years has unraveled some of the underlying principles of these pathways and underscored the important role of DNA damage in polyploidization. Furthermore, polyploidization per se may also be an important determinant of sensitivity to DNA damage, thereby may offer an opportunity for novel therapies.